Back to Long Tests report for BioC 3.23

This page was generated on 2025-11-22 23:55 -0500 (Sat, 22 Nov 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_64R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" 4829
lconwaymacOS 12.7.6 Montereyx86_64R Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences" 4603
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 6/28HostnameOS / ArchCHECK
biodbChebi 1.17.0  (landing page)
Pierrick Roger
Snapshot Date: 2025-11-22 09:55 -0500 (Sat, 22 Nov 2025)
git_url: https://git.bioconductor.org/packages/biodbChebi
git_branch: devel
git_last_commit: 80ee611
git_last_commit_date: 2025-10-29 11:12:25 -0500 (Wed, 29 Oct 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  ERROR  
lconwaymacOS 12.7.6 Monterey / x86_64  ERROR  

CHECK results for biodbChebi on nebbiolo1

To the developers/maintainers of the biodbChebi 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: biodbChebi
Version: 1.17.0
Command: /home/biocbuild/bbs-3.23-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 biodbChebi_1.17.0.tar.gz
StartedAt: 2025-11-22 16:01:05 -0500 (Sat, 22 Nov 2025)
EndedAt: 2025-11-22 16:02:15 -0500 (Sat, 22 Nov 2025)
EllapsedTime: 70.0 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbChebi.Rcheck
Warnings: NA

Tests output

biodbChebi.Rcheck/tests/testthat.Rout.fail


R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbChebi)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbChebi")
biodb.INFO [2025-11-22 16:01:42.895][biodb::testContext]
biodb.INFO [2025-11-22 16:01:42.897][biodb::testContext] ********************************************************************************
biodb.INFO [2025-11-22 16:01:42.898][biodb::testContext] Test context - Generic long tests
biodb.INFO [2025-11-22 16:01:42.899][biodb::testContext] ********************************************************************************
biodb.INFO [2025-11-22 16:01:42.900][biodb::testContext]
biodb.INFO [2025-11-22 16:01:42.905][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.19.0.
biodb.DEBUG[2025-11-22 16:01:42.907][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.23-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-11-22 16:01:42.914][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-11-22 16:01:42.915][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-11-22 16:01:42.916][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-11-22 16:01:42.917][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:01:42.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:01:42.918][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:01:42.919][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-11-22 16:01:42.936][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-11-22 16:01:42.937][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:01:42.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:01:42.938][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:01:42.939][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-11-22 16:01:42.940][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-11-22 16:01:42.941][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:01:42.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:01:42.943][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:01:42.944][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-11-22 16:01:42.945][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-11-22 16:01:42.946][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-11-22 16:01:42.947][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:01:42.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:01:42.948][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:01:42.949][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-11-22 16:01:42.950][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-11-22 16:01:42.951][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-11-22 16:01:42.952][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:01:42.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:01:42.954][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:01:42.955][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-11-22 16:01:42.956][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-11-22 16:01:42.957][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:01:42.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:01:42.958][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:01:42.959][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-11-22 16:01:42.960][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-11-22 16:01:42.961][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-11-22 16:01:42.962][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:01:42.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:01:42.964][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:01:42.965][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-11-22 16:01:42.966][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-11-22 16:01:42.967][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:01:42.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:01:42.968][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:01:42.969][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-11-22 16:01:42.970][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-11-22 16:01:42.971][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-11-22 16:01:42.972][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:01:42.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:01:42.974][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:01:42.975][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-11-22 16:01:42.976][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-11-22 16:01:42.977][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-11-22 16:01:42.978][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-11-22 16:01:42.979][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-11-22 16:01:42.980][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-11-22 16:01:42.980][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:01:42.981][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:01:42.982][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:01:42.983][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-11-22 16:01:42.984][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-11-22 16:01:42.985][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:01:42.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:01:42.987][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:01:42.988][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-11-22 16:01:42.989][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-11-22 16:01:42.989][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:01:42.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:01:42.991][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:01:42.992][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-11-22 16:01:42.993][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-11-22 16:01:42.994][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:01:42.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:01:42.996][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:01:42.997][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-11-22 16:01:42.997][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-11-22 16:01:42.998][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-11-22 16:01:42.999][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:01:43.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:01:43.001][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:01:43.002][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-11-22 16:01:43.003][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-11-22 16:01:43.007][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-11-22 16:01:43.008][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:01:43.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:01:43.010][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:01:43.011][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-11-22 16:01:43.012][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-11-22 16:01:43.013][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-11-22 16:01:43.014][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:01:43.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:01:43.015][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:01:43.019][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-11-22 16:01:43.049][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-11-22 16:01:43.064][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-11-22 16:01:43.065][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-22 16:01:43.066][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-22 16:01:43.067][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-22 16:01:43.068][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-22 16:01:43.068][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-11-22 16:01:43.069][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-22 16:01:43.070][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-11-22 16:01:43.071][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-22 16:01:43.072][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-11-22 16:01:43.073][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-11-22 16:01:43.074][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-22 16:01:43.075][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-11-22 16:01:43.076][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-11-22 16:01:43.077][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-11-22 16:01:43.077][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-11-22 16:01:43.077][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-11-22 16:01:43.077][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-11-22 16:01:43.077][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-11-22 16:01:43.078][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-11-22 16:01:43.079][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:01:43.080][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:01:43.087][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-22 16:01:43.088][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:01:43.088][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:01:43.089][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-22 16:01:43.090][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-11-22 16:01:43.091][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-22 16:01:43.093][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-22 16:01:43.093][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-11-22 16:01:43.094][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-22 16:01:43.095][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-11-22 16:01:43.097][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-11-22 16:01:43.098][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-11-22 16:01:43.099][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-22 16:01:43.100][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-22 16:01:43.101][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-22 16:01:43.102][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-22 16:01:43.103][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-11-22 16:01:43.104][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-22 16:01:43.105][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-11-22 16:01:43.106][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-22 16:01:43.106][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-11-22 16:01:43.107][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-11-22 16:01:43.108][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-22 16:01:43.109][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-11-22 16:01:43.110][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-11-22 16:01:43.111][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-11-22 16:01:43.111][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-11-22 16:01:43.111][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-11-22 16:01:43.111][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-11-22 16:01:43.111][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-11-22 16:01:43.112][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-11-22 16:01:43.113][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:01:43.114][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:01:43.115][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-22 16:01:43.116][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:01:43.117][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:01:43.118][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-22 16:01:43.119][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-11-22 16:01:43.119][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-22 16:01:43.120][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-22 16:01:43.121][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-11-22 16:01:43.122][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-22 16:01:43.124][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-11-22 16:01:43.125][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-11-22 16:01:43.126][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-11-22 16:01:43.127][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-22 16:01:43.128][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-22 16:01:43.129][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-22 16:01:43.130][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-22 16:01:43.131][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-11-22 16:01:43.132][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-22 16:01:43.133][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-11-22 16:01:43.134][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-22 16:01:43.135][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-11-22 16:01:43.136][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-11-22 16:01:43.137][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-22 16:01:43.138][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-11-22 16:01:43.139][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-11-22 16:01:43.140][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-11-22 16:01:43.141][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-11-22 16:01:43.142][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:01:43.143][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:01:43.144][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-22 16:01:43.145][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:01:43.145][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:01:43.146][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-22 16:01:43.147][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-11-22 16:01:43.148][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-22 16:01:43.149][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-22 16:01:43.150][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-11-22 16:01:43.151][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-22 16:01:43.152][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-11-22 16:01:43.154][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-11-22 16:01:43.155][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-11-22 16:01:43.156][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-22 16:01:43.157][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-22 16:01:43.157][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-22 16:01:43.158][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-22 16:01:43.159][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-11-22 16:01:43.160][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-11-22 16:01:43.161][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-11-22 16:01:43.162][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-22 16:01:43.163][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-11-22 16:01:43.164][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-11-22 16:01:43.165][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-22 16:01:43.166][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-11-22 16:01:43.167][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-11-22 16:01:43.168][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-11-22 16:01:43.169][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-11-22 16:01:43.170][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:01:43.171][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:01:43.172][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-22 16:01:43.173][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:01:43.173][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:01:43.174][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-22 16:01:43.175][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-11-22 16:01:43.176][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-22 16:01:43.177][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-22 16:01:43.178][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-11-22 16:01:43.179][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-11-22 16:01:43.183][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-11-22 16:01:43.184][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:01:43.184][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:01:43.185][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:01:43.186][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:01:43.187][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:01:43.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:01:43.189][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:01:43.190][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:01:43.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:01:43.191][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:01:43.192][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:01:43.193][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:01:43.194][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:01:43.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:01:43.196][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:01:43.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:01:43.197][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:01:43.198][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:01:43.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:01:43.200][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:01:43.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:01:43.202][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:01:43.203][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:01:43.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:01:43.204][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:01:43.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:01:43.206][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:01:43.207][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:01:43.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:01:43.215][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:01:43.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:01:43.218][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:01:43.219][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:01:43.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:01:43.221][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:01:43.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:01:43.223][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:01:43.224][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:01:43.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:01:43.226][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:01:43.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:01:43.228][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:01:43.229][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:01:43.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:01:43.231][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:01:43.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:01:43.233][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:01:43.234][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:01:43.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:01:43.236][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:01:43.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:01:43.238][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:01:43.239][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:01:43.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:01:43.241][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:01:43.242][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:01:43.243][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:01:43.244][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:01:43.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:01:43.246][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:01:43.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:01:43.248][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:01:43.249][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:01:43.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:01:43.250][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:01:43.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:01:43.252][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:01:43.253][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:01:43.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:01:43.255][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:01:43.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:01:43.257][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:01:43.258][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:01:43.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:01:43.260][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:01:43.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:01:43.262][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:01:43.263][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:01:43.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:01:43.265][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:01:43.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:01:43.267][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:01:43.268][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-11-22 16:01:43.274][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-11-22 16:01:43.275][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-11-22 16:01:43.277][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-11-22 16:01:43.278][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-11-22 16:01:43.280][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-11-22 16:01:43.281][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-11-22 16:01:43.283][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-11-22 16:01:43.284][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-11-22 16:01:43.285][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-11-22 16:01:43.287][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-11-22 16:01:43.288][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-11-22 16:01:43.290][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-11-22 16:01:43.291][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-11-22 16:01:43.293][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-11-22 16:01:43.294][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-11-22 16:01:43.313][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-11-22 16:01:43.315][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-11-22 16:01:43.316][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-11-22 16:01:43.318][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-11-22 16:01:43.319][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-11-22 16:01:43.321][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-11-22 16:01:43.322][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-11-22 16:01:43.323][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-11-22 16:01:43.325][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-11-22 16:01:43.326][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-11-22 16:01:43.328][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-11-22 16:01:43.329][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-11-22 16:01:43.331][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-11-22 16:01:43.332][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-11-22 16:01:43.334][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-11-22 16:01:43.335][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-11-22 16:01:43.337][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-11-22 16:01:43.338][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-11-22 16:01:43.340][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-11-22 16:01:43.341][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-11-22 16:01:43.343][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-11-22 16:01:43.344][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-11-22 16:01:43.345][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-11-22 16:01:43.347][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-11-22 16:01:43.349][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-11-22 16:01:43.350][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-11-22 16:01:43.352][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-11-22 16:01:43.353][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-11-22 16:01:43.355][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-11-22 16:01:43.356][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-11-22 16:01:43.358][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-11-22 16:01:43.359][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-11-22 16:01:43.361][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-11-22 16:01:43.362][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-11-22 16:01:43.364][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-11-22 16:01:43.365][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-11-22 16:01:43.366][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-11-22 16:01:43.368][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-11-22 16:01:43.369][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-11-22 16:01:43.371][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-11-22 16:01:43.372][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-11-22 16:01:43.374][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-11-22 16:01:43.375][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-11-22 16:01:43.377][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-11-22 16:01:43.378][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-11-22 16:01:43.379][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-11-22 16:01:43.381][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-11-22 16:01:43.382][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-11-22 16:01:43.384][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-11-22 16:01:43.385][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-11-22 16:01:43.387][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-11-22 16:01:43.388][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-11-22 16:01:43.390][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-11-22 16:01:43.391][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-11-22 16:01:43.392][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-11-22 16:01:43.394][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-11-22 16:01:43.395][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-11-22 16:01:43.397][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-11-22 16:01:43.398][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-11-22 16:01:43.400][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-11-22 16:01:43.401][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-11-22 16:01:43.403][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-11-22 16:01:43.404][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-11-22 16:01:43.405][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-11-22 16:01:43.407][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-11-22 16:01:43.408][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-11-22 16:01:43.410][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-11-22 16:01:43.416][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-11-22 16:01:43.418][initialize] This is biodb version 1.19.0.
biodb.DEBUG[2025-11-22 16:01:43.421][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-11-22 16:01:43.422][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:01:43.423][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:01:43.424][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:01:43.425][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:01:43.430][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:01:43.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:01:43.432][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:01:43.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:01:43.434][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:01:43.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:01:43.436][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:01:43.437][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:01:43.438][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:01:43.439][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:01:43.440][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:01:43.440][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:01:43.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:01:43.442][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:01:43.443][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:01:43.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:01:43.445][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:01:43.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:01:43.447][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:01:43.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:01:43.448][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:01:43.449][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:01:43.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:01:43.451][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:01:43.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:01:43.453][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:01:43.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:01:43.454][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:01:43.455][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:01:43.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:01:43.457][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:01:43.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:01:43.459][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:01:43.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:01:43.460][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:01:43.461][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:01:43.462][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:01:43.463][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:01:43.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:01:43.465][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:01:43.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:01:43.467][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:01:43.467][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:01:43.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:01:43.469][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:01:43.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:01:43.471][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:01:43.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:01:43.473][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:01:43.473][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:01:43.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:01:43.475][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:01:43.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:01:43.477][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:01:43.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:01:43.479][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:01:43.480][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:01:43.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:01:43.481][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:01:43.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:01:43.483][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:01:43.484][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:01:43.485][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[2025-11-22 16:01:43.486][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:01:43.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:01:43.487][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:01:43.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:01:43.489][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:01:43.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:01:43.491][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:01:43.492][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:01:43.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:01:43.493][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:01:43.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:01:43.495][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:01:43.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:01:43.497][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:01:43.498][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:01:43.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:01:43.500][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:01:43.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:01:43.501][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:01:43.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:01:43.503][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:01:43.504][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:01:43.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:01:43.506][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:01:43.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:01:43.507][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:01:43.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:01:43.514][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[2025-11-22 16:01:43.515][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:01:43.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:01:43.516][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:01:43.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:01:43.518][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:01:43.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:01:43.520][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:01:43.521][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:01:43.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:01:43.522][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:01:43.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:01:43.524][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:01:43.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:01:43.526][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:01:43.527][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-11-22 16:01:43.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:01:43.528][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:01:43.529][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:01:43.530][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:01:43.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:01:43.532][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-11-22 16:01:43.534][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.23-bioc-longtests/meat/biodbChebi.Rcheck/biodbChebi/definitions.yml".
biodb.DEBUG[2025-11-22 16:01:43.543][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-11-22 16:01:43.545][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-11-22 16:01:43.546][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-11-22 16:01:43.547][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-11-22 16:01:43.548][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-11-22 16:01:43.549][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-11-22 16:01:43.550][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-11-22 16:01:43.551][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-11-22 16:01:43.552][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-11-22 16:01:43.553][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-11-22 16:01:43.554][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-11-22 16:01:43.555][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-11-22 16:01:43.556][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-11-22 16:01:43.557][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-11-22 16:01:43.558][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-11-22 16:01:43.558][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-11-22 16:01:43.558][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-11-22 16:01:43.558][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-11-22 16:01:43.558][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-11-22 16:01:43.558][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-11-22 16:01:43.558][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-11-22 16:01:43.558][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-11-22 16:01:43.558][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-11-22 16:01:43.558][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-11-22 16:01:43.558][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-11-22 16:01:43.559][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-11-22 16:01:43.560][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-11-22 16:01:43.560][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-11-22 16:01:43.560][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-11-22 16:01:43.561][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-11-22 16:01:43.562][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:01:43.563][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:01:43.564][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-11-22 16:01:43.565][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-11-22 16:01:43.566][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-11-22 16:01:43.567][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-11-22 16:01:43.568][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-11-22 16:01:43.568][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-11-22 16:01:43.569][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-11-22 16:01:43.569][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-11-22 16:01:43.570][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-11-22 16:01:43.571][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-11-22 16:01:43.571][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-11-22 16:01:43.577][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-11-22 16:01:43.579][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-11-22 16:01:43.580][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-11-22 16:01:43.582][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-11-22 16:01:43.583][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-11-22 16:01:43.585][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-11-22 16:01:43.606][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-11-22 16:01:43.621][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-11-22 16:01:43.629][biodb::testThat]
biodb.INFO [2025-11-22 16:01:43.630][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-11-22 16:01:43.631][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-22 16:01:43.632][biodb::testThat]
biodb.TRACE[2025-11-22 16:01:43.635][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.23-bioc-longtests/meat/biodbChebi.Rcheck/biodbChebi/testref/entry-chebi-15440-content.xml".
biodb.DEBUG[2025-11-22 16:01:43.637][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-11-22 16:01:43.640][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-11-22 16:01:43.648][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-11-22 16:01:43.649][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:01:43.649][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:01:43.662][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:01:43.663][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:01:43.664][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:01:43.664][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-11-22 16:01:43.673][ef$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:01:43.674][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:01:43.675][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:43.676][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:43.678][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:01:43.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:01:43.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:43.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:43.693][ef$get] Asked field names are: charge.
biodb.TRACE[2025-11-22 16:01:43.694][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-11-22 16:01:43.695][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:43.696][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:43.729][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-11-22 16:01:43.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-11-22 16:01:43.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:43.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:43.733][ef$get] Asked field names are: formula.
biodb.TRACE[2025-11-22 16:01:43.734][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-22 16:01:43.735][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:43.736][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:43.737][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-22 16:01:43.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-22 16:01:43.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:43.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:43.741][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:01:43.742][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:01:43.743][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:43.744][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:43.745][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:01:43.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:01:43.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:43.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:43.749][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:01:43.750][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:01:43.751][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:43.752][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:43.753][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:01:43.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:01:43.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:43.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:43.757][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:01:43.758][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:01:43.759][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:43.760][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:43.761][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:01:43.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:01:43.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:43.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:43.765][ef$get] Asked field names are: mass.
biodb.TRACE[2025-11-22 16:01:43.766][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:01:43.767][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:43.768][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:43.769][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-11-22 16:01:43.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:01:43.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:43.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:43.773][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:01:43.774][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:01:43.775][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:43.776][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:43.777][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:01:43.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:01:43.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:43.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:43.781][ef$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:01:43.782][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:01:43.783][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:43.784][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:43.785][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:01:43.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:01:43.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:43.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:43.789][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-11-22 16:01:43.790][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-11-22 16:01:43.791][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:43.792][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:43.793][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-11-22 16:01:43.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-11-22 16:01:43.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:43.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:43.797][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-11-22 16:01:43.798][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-22 16:01:43.799][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:43.799][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:43.801][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-11-22 16:01:43.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-22 16:01:43.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:43.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:43.805][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-22 16:01:43.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-22 16:01:43.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:43.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:43.808][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-22 16:01:43.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-22 16:01:43.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:43.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:43.812][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:01:43.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:01:43.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:43.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:43.816][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-22 16:01:43.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-22 16:01:43.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:43.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:43.820][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:01:43.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:01:43.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:43.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:43.824][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:01:43.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:01:43.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:43.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:43.828][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:01:43.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:01:43.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:43.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:43.862][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:01:43.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:01:43.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:43.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:43.866][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:01:43.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:01:43.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:43.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:43.874][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:01:43.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:01:43.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:43.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-11-22 16:01:43.877][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440.
biodb.TRACE[2025-11-22 16:01:43.880][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:01:43.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:01:43.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:43.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:43.884][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:01:43.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:01:43.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:43.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:43.909][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:01:43.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:01:43.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:43.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:43.913][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:01:43.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:01:43.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:43.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:43.916][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-22 16:01:43.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:01:43.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:43.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:43.920][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-22 16:01:43.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:01:43.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:43.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:43.924][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-11-22 16:01:43.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-11-22 16:01:43.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:43.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:43.928][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-11-22 16:01:43.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-11-22 16:01:43.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:43.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:43.932][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-11-22 16:01:43.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-11-22 16:01:43.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:43.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:43.935][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-11-22 16:01:43.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-11-22 16:01:43.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:43.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:43.941][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:01:43.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:01:43.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:43.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:43.957][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-22 16:01:43.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-22 16:01:43.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:43.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:43.964][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:01:43.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:01:43.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:43.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:43.968][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:01:43.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:01:43.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:43.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:43.972][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:01:43.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:01:43.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:43.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:43.977][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:01:43.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:01:43.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:43.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:43.981][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:01:43.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:01:43.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:43.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:43.985][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:01:43.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:01:43.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:43.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:43.989][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-22 16:01:43.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-22 16:01:43.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:43.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:43.992][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-22 16:01:43.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-22 16:01:43.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:43.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:43.996][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-22 16:01:43.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-22 16:01:43.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:43.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.006][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:01:44.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:01:44.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.010][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:01:44.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:01:44.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.014][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:01:44.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:01:44.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.018][ef$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:01:44.019][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:01:44.054][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.056][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.056][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:01:44.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:01:44.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.067][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-22 16:01:44.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-22 16:01:44.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.071][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-22 16:01:44.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-22 16:01:44.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.075][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-22 16:01:44.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-22 16:01:44.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.079][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-22 16:01:44.080][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-22 16:01:44.081][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.082][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.083][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-22 16:01:44.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-22 16:01:44.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.093][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:01:44.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:01:44.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.097][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:01:44.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:01:44.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.101][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:01:44.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:01:44.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.105][ef$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:01:44.106][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:01:44.107][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.107][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.108][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:01:44.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:01:44.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.119][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-22 16:01:44.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-22 16:01:44.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.123][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-22 16:01:44.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-22 16:01:44.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.127][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-22 16:01:44.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-22 16:01:44.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.130][ef$get] Asked field names are: formula.
biodb.TRACE[2025-11-22 16:01:44.131][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-22 16:01:44.132][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.133][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.134][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-22 16:01:44.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-22 16:01:44.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.145][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-22 16:01:44.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:01:44.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.149][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-22 16:01:44.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:01:44.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.152][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-22 16:01:44.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:01:44.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.156][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-22 16:01:44.157][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:01:44.158][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.159][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.160][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-22 16:01:44.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:01:44.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.170][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:01:44.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:01:44.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.174][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:01:44.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:01:44.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.178][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:01:44.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:01:44.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.182][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:01:44.183][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:01:44.184][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.185][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.186][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:01:44.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:01:44.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.196][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-11-22 16:01:44.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-11-22 16:01:44.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.200][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-11-22 16:01:44.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-11-22 16:01:44.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.204][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-11-22 16:01:44.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-11-22 16:01:44.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.211][ef$get] Asked field names are: charge.
biodb.TRACE[2025-11-22 16:01:44.212][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-11-22 16:01:44.213][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.214][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.215][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-11-22 16:01:44.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-11-22 16:01:44.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.225][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-11-22 16:01:44.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-11-22 16:01:44.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.229][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-11-22 16:01:44.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-11-22 16:01:44.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.233][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-11-22 16:01:44.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-11-22 16:01:44.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.237][ef$get] Asked field names are: n.stars.
biodb.TRACE[2025-11-22 16:01:44.238][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-11-22 16:01:44.239][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.240][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.241][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-11-22 16:01:44.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-11-22 16:01:44.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.251][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:01:44.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:01:44.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.255][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:01:44.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:01:44.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.259][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:01:44.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:01:44.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.262][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:01:44.263][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:01:44.264][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.265][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.266][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:01:44.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:01:44.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.277][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-11-22 16:01:44.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-22 16:01:44.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.280][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-11-22 16:01:44.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-22 16:01:44.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.284][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-11-22 16:01:44.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-22 16:01:44.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.288][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-11-22 16:01:44.289][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-22 16:01:44.290][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.291][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.292][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-11-22 16:01:44.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-22 16:01:44.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.302][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:01:44.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:01:44.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.306][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:01:44.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:01:44.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.310][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:01:44.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:01:44.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.314][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:01:44.315][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:01:44.316][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.317][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.318][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:01:44.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:01:44.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.328][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:01:44.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:01:44.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.332][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:01:44.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:01:44.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.336][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:01:44.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:01:44.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.340][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:01:44.341][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:01:44.342][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.343][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.344][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:01:44.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:01:44.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.355][ef$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:01:44.356][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:01:44.357][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.358][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.362][ef$get] Asked field names are: charge.
biodb.TRACE[2025-11-22 16:01:44.363][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-11-22 16:01:44.364][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.369][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.373][ef$get] Asked field names are: formula.
biodb.TRACE[2025-11-22 16:01:44.374][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-22 16:01:44.374][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.375][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.379][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:01:44.380][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:01:44.381][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.382][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.386][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:01:44.387][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:01:44.388][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.389][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.392][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:01:44.393][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:01:44.394][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.395][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.399][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-22 16:01:44.400][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:01:44.401][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.402][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.406][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:01:44.407][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:01:44.408][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.409][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.413][ef$get] Asked field names are: n.stars.
biodb.TRACE[2025-11-22 16:01:44.414][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-11-22 16:01:44.415][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.415][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.419][ef$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:01:44.420][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:01:44.421][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.422][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.426][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-11-22 16:01:44.427][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-22 16:01:44.428][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.429][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.445][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.23-bioc-longtests/meat/biodbChebi.Rcheck/biodbChebi/testref/entry-chebi-2528-content.xml".
biodb.DEBUG[2025-11-22 16:01:44.478][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-11-22 16:01:44.479][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-11-22 16:01:44.480][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-11-22 16:01:44.481][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:01:44.482][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:01:44.486][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:01:44.487][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:01:44.488][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:01:44.489][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-11-22 16:01:44.491][ef$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:01:44.492][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:01:44.493][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.494][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.495][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:01:44.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:01:44.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.518][ef$get] Asked field names are: charge.
biodb.TRACE[2025-11-22 16:01:44.519][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-11-22 16:01:44.520][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.520][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.522][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-11-22 16:01:44.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-11-22 16:01:44.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.526][ef$get] Asked field names are: formula.
biodb.TRACE[2025-11-22 16:01:44.527][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-22 16:01:44.527][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.528][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.530][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-22 16:01:44.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-22 16:01:44.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.534][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:01:44.535][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:01:44.536][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.537][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.538][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:01:44.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:01:44.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.542][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:01:44.543][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:01:44.544][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.544][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.546][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:01:44.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:01:44.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.550][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:01:44.551][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:01:44.551][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.552][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.553][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:01:44.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:01:44.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.557][ef$get] Asked field names are: mass.
biodb.TRACE[2025-11-22 16:01:44.558][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:01:44.559][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.560][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.561][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-11-22 16:01:44.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:01:44.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.565][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:01:44.566][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:01:44.567][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.568][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.569][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:01:44.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:01:44.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.573][ef$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:01:44.574][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:01:44.575][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.576][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.577][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:01:44.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:01:44.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.581][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-11-22 16:01:44.582][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-11-22 16:01:44.583][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.584][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.585][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-11-22 16:01:44.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-11-22 16:01:44.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.589][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-11-22 16:01:44.590][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-22 16:01:44.591][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.592][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.593][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-11-22 16:01:44.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-22 16:01:44.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.597][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-22 16:01:44.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-22 16:01:44.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.601][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-22 16:01:44.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-22 16:01:44.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.604][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:01:44.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:01:44.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.608][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-22 16:01:44.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-22 16:01:44.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.612][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:01:44.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:01:44.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.616][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:01:44.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:01:44.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.620][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:01:44.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:01:44.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.624][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:01:44.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:01:44.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.628][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:01:44.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:01:44.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.631][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:01:44.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:01:44.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-11-22 16:01:44.635][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 2528.
biodb.TRACE[2025-11-22 16:01:44.654][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:01:44.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:01:44.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.662][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:01:44.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:01:44.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.666][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:01:44.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:01:44.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.670][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:01:44.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:01:44.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.673][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-22 16:01:44.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:01:44.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.677][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-22 16:01:44.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:01:44.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.681][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-11-22 16:01:44.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-11-22 16:01:44.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.685][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-11-22 16:01:44.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-11-22 16:01:44.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.688][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-11-22 16:01:44.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-11-22 16:01:44.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.692][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-11-22 16:01:44.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-11-22 16:01:44.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.697][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:01:44.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:01:44.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.704][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-22 16:01:44.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-22 16:01:44.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.711][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:01:44.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:01:44.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.715][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:01:44.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:01:44.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.719][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:01:44.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:01:44.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.724][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:01:44.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:01:44.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.728][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:01:44.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:01:44.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.731][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:01:44.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:01:44.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.736][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-22 16:01:44.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-22 16:01:44.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.739][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-22 16:01:44.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-22 16:01:44.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.743][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-22 16:01:44.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-22 16:01:44.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.762][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:01:44.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:01:44.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.765][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:01:44.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:01:44.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.769][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:01:44.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:01:44.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.773][ef$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:01:44.774][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:01:44.775][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.776][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.777][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:01:44.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:01:44.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.787][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-22 16:01:44.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-22 16:01:44.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.791][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-22 16:01:44.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-22 16:01:44.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.795][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-22 16:01:44.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-22 16:01:44.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.799][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-22 16:01:44.800][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-22 16:01:44.801][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.802][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.802][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-22 16:01:44.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-22 16:01:44.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.817][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:01:44.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:01:44.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.821][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:01:44.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:01:44.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.825][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:01:44.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:01:44.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.828][ef$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:01:44.829][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:01:44.830][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.831][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.832][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:01:44.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:01:44.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.842][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-22 16:01:44.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-22 16:01:44.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.846][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-22 16:01:44.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-22 16:01:44.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.850][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-22 16:01:44.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-22 16:01:44.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.854][ef$get] Asked field names are: formula.
biodb.TRACE[2025-11-22 16:01:44.855][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-22 16:01:44.856][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.857][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.858][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-22 16:01:44.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-22 16:01:44.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.868][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-11-22 16:01:44.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:01:44.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.872][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-22 16:01:44.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:01:44.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.875][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-22 16:01:44.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:01:44.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.879][ef$get] Asked field names are: mass.
biodb.TRACE[2025-11-22 16:01:44.880][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:01:44.881][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.882][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.883][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-11-22 16:01:44.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:01:44.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.893][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:01:44.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:01:44.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.897][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:01:44.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:01:44.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.901][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:01:44.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:01:44.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.905][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:01:44.906][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:01:44.907][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.908][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.909][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:01:44.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:01:44.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.919][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-22 16:01:44.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:01:44.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.923][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-22 16:01:44.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:01:44.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.927][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-22 16:01:44.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:01:44.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.931][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-22 16:01:44.932][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:01:44.932][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.933][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.934][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-22 16:01:44.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:01:44.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.945][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-11-22 16:01:44.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-11-22 16:01:44.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.948][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-11-22 16:01:44.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-11-22 16:01:44.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.952][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-11-22 16:01:44.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-11-22 16:01:44.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.956][ef$get] Asked field names are: charge.
biodb.TRACE[2025-11-22 16:01:44.957][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-11-22 16:01:44.958][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.959][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.960][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-11-22 16:01:44.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-11-22 16:01:44.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.974][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-11-22 16:01:44.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-11-22 16:01:44.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.978][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-11-22 16:01:44.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-11-22 16:01:44.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.982][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-11-22 16:01:44.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-11-22 16:01:44.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.986][ef$get] Asked field names are: n.stars.
biodb.TRACE[2025-11-22 16:01:44.987][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-11-22 16:01:44.988][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.989][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:44.990][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-11-22 16:01:44.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-11-22 16:01:44.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:44.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.000][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:01:45.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:01:45.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.004][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:01:45.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:01:45.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.008][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:01:45.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:01:45.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.011][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:01:45.012][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:01:45.013][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.014][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.015][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:01:45.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:01:45.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.025][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-11-22 16:01:45.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-22 16:01:45.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.029][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-11-22 16:01:45.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-22 16:01:45.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.033][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-11-22 16:01:45.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-22 16:01:45.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.037][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-11-22 16:01:45.038][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-22 16:01:45.039][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.040][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.041][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-11-22 16:01:45.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-22 16:01:45.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.051][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:01:45.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:01:45.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.055][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:01:45.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:01:45.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.059][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:01:45.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:01:45.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.063][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:01:45.064][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:01:45.065][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.066][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.067][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:01:45.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:01:45.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.077][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:01:45.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:01:45.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.081][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:01:45.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:01:45.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.085][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:01:45.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:01:45.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.089][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:01:45.090][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:01:45.090][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.091][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.092][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:01:45.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:01:45.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.103][ef$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:01:45.104][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:01:45.105][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.106][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.110][ef$get] Asked field names are: charge.
biodb.TRACE[2025-11-22 16:01:45.111][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-11-22 16:01:45.112][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.112][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.116][ef$get] Asked field names are: formula.
biodb.TRACE[2025-11-22 16:01:45.117][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-22 16:01:45.118][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.123][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.127][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:01:45.128][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:01:45.129][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.130][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.134][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:01:45.135][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:01:45.136][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.137][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.140][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:01:45.141][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:01:45.142][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.143][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.147][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-22 16:01:45.148][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:01:45.149][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.150][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.154][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:01:45.155][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:01:45.156][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.156][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.160][ef$get] Asked field names are: n.stars.
biodb.TRACE[2025-11-22 16:01:45.161][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-11-22 16:01:45.162][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.163][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.167][ef$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:01:45.168][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:01:45.169][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.170][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.174][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-11-22 16:01:45.175][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-22 16:01:45.176][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.177][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.181][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.23-bioc-longtests/meat/biodbChebi.Rcheck/biodbChebi/testref/entry-chebi-7799-content.xml".
biodb.DEBUG[2025-11-22 16:01:45.182][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-11-22 16:01:45.183][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-11-22 16:01:45.185][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-11-22 16:01:45.185][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:01:45.186][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:01:45.190][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:01:45.191][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:01:45.192][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:01:45.193][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-11-22 16:01:45.195][ef$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:01:45.196][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:01:45.197][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.198][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.199][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:01:45.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:01:45.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.203][ef$get] Asked field names are: charge.
biodb.TRACE[2025-11-22 16:01:45.204][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-11-22 16:01:45.205][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.206][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.207][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-11-22 16:01:45.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-11-22 16:01:45.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.211][ef$get] Asked field names are: formula.
biodb.TRACE[2025-11-22 16:01:45.212][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-22 16:01:45.213][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.214][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.215][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-22 16:01:45.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-22 16:01:45.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.219][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:01:45.220][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:01:45.221][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.222][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.223][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:01:45.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:01:45.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.227][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:01:45.228][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:01:45.229][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.230][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.231][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:01:45.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:01:45.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.235][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:01:45.236][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:01:45.237][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.238][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.239][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:01:45.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:01:45.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.243][ef$get] Asked field names are: mass.
biodb.TRACE[2025-11-22 16:01:45.244][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:01:45.245][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.246][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.247][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-11-22 16:01:45.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:01:45.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.251][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:01:45.252][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:01:45.253][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.253][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.255][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:01:45.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:01:45.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.258][ef$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:01:45.259][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:01:45.260][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.261][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.263][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:01:45.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:01:45.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.267][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-11-22 16:01:45.268][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-11-22 16:01:45.268][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.269][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.271][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-11-22 16:01:45.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-11-22 16:01:45.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.274][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-11-22 16:01:45.275][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-22 16:01:45.280][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.281][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.282][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-11-22 16:01:45.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-22 16:01:45.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.286][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-22 16:01:45.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-22 16:01:45.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.290][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-22 16:01:45.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-22 16:01:45.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.294][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:01:45.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:01:45.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.298][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-22 16:01:45.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-22 16:01:45.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.301][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:01:45.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:01:45.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.305][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:01:45.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:01:45.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.309][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:01:45.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:01:45.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.313][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:01:45.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:01:45.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.317][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:01:45.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:01:45.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.321][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:01:45.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:01:45.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-11-22 16:01:45.324][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 7799.
biodb.TRACE[2025-11-22 16:01:45.326][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:01:45.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:01:45.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.330][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:01:45.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:01:45.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.334][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:01:45.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:01:45.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.338][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:01:45.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:01:45.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.342][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-22 16:01:45.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:01:45.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.346][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-22 16:01:45.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:01:45.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.349][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-11-22 16:01:45.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-11-22 16:01:45.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.353][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-11-22 16:01:45.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-11-22 16:01:45.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.357][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-11-22 16:01:45.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-11-22 16:01:45.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.361][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-11-22 16:01:45.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-11-22 16:01:45.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.366][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:01:45.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:01:45.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.373][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-22 16:01:45.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-22 16:01:45.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.380][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:01:45.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:01:45.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.384][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:01:45.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:01:45.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.388][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:01:45.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:01:45.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.393][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:01:45.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:01:45.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.397][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:01:45.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:01:45.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.401][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:01:45.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:01:45.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.405][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-22 16:01:45.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-22 16:01:45.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.408][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-22 16:01:45.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-22 16:01:45.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.412][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-22 16:01:45.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-22 16:01:45.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.421][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:01:45.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:01:45.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.425][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:01:45.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:01:45.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.429][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:01:45.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:01:45.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.432][ef$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:01:45.434][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:01:45.434][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.439][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.440][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:01:45.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:01:45.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.451][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-11-22 16:01:45.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-22 16:01:45.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.454][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-11-22 16:01:45.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-22 16:01:45.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.458][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-11-22 16:01:45.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-22 16:01:45.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.462][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-11-22 16:01:45.463][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-22 16:01:45.464][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.465][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.466][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-11-22 16:01:45.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-22 16:01:45.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.476][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:01:45.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:01:45.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.480][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:01:45.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:01:45.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.484][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:01:45.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:01:45.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.488][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:01:45.489][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:01:45.490][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.491][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.492][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:01:45.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:01:45.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.502][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:01:45.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:01:45.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.506][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:01:45.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:01:45.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.510][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:01:45.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:01:45.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.514][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:01:45.515][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:01:45.516][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.517][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.518][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:01:45.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:01:45.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.528][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:01:45.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:01:45.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.532][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:01:45.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:01:45.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.536][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:01:45.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:01:45.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.540][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:01:45.541][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:01:45.542][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.543][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.544][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:01:45.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:01:45.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.554][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-22 16:01:45.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:01:45.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.558][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-22 16:01:45.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:01:45.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.562][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-22 16:01:45.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:01:45.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.566][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-22 16:01:45.567][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:01:45.568][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.569][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.570][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-22 16:01:45.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:01:45.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.580][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:01:45.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:01:45.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.584][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:01:45.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:01:45.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.588][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:01:45.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:01:45.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.596][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:01:45.597][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:01:45.598][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.599][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.600][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:01:45.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:01:45.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.610][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-11-22 16:01:45.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-11-22 16:01:45.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.614][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-11-22 16:01:45.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-11-22 16:01:45.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.618][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-11-22 16:01:45.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-11-22 16:01:45.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.622][ef$get] Asked field names are: charge.
biodb.TRACE[2025-11-22 16:01:45.623][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-11-22 16:01:45.624][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.624][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.625][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-11-22 16:01:45.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-11-22 16:01:45.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.636][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-11-22 16:01:45.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-11-22 16:01:45.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.640][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-11-22 16:01:45.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-11-22 16:01:45.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.644][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-11-22 16:01:45.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-11-22 16:01:45.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.648][ef$get] Asked field names are: n.stars.
biodb.TRACE[2025-11-22 16:01:45.649][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-11-22 16:01:45.650][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.651][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.652][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-11-22 16:01:45.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-11-22 16:01:45.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.662][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:01:45.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:01:45.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.666][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:01:45.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:01:45.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.670][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:01:45.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:01:45.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.674][ef$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:01:45.675][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:01:45.676][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.677][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.678][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:01:45.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:01:45.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.689][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-22 16:01:45.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-22 16:01:45.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.693][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-22 16:01:45.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-22 16:01:45.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.696][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-22 16:01:45.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-22 16:01:45.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.700][ef$get] Asked field names are: formula.
biodb.TRACE[2025-11-22 16:01:45.701][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-22 16:01:45.702][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.703][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.704][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-11-22 16:01:45.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-22 16:01:45.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.715][ef$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:01:45.716][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:01:45.717][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.718][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.721][ef$get] Asked field names are: charge.
biodb.TRACE[2025-11-22 16:01:45.722][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-11-22 16:01:45.723][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.724][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.728][ef$get] Asked field names are: formula.
biodb.TRACE[2025-11-22 16:01:45.729][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-11-22 16:01:45.730][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.731][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.735][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-11-22 16:01:45.736][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-11-22 16:01:45.737][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.738][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.742][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-11-22 16:01:45.743][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-11-22 16:01:45.744][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.745][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.753][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:01:45.754][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-11-22 16:01:45.755][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.756][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.760][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-11-22 16:01:45.761][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-11-22 16:01:45.762][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.763][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.767][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:01:45.768][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:01:45.769][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.770][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.774][ef$get] Asked field names are: n.stars.
biodb.TRACE[2025-11-22 16:01:45.775][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-11-22 16:01:45.776][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.777][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.780][ef$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:01:45.781][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:01:45.782][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.783][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:01:45.787][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-11-22 16:01:45.788][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-11-22 16:01:45.789][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:01:45.790][ef$get] fields variable is a list.
biodb.INFO [2025-11-22 16:01:45.797][biodb::testThat]
biodb.INFO [2025-11-22 16:01:45.798][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-11-22 16:01:45.798][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-22 16:01:45.799][biodb::testThat]
biodb.DEBUG[2025-11-22 16:01:45.801][private$loadEntries] Creating entries from ids [3]: "15440, 2528, 7799".
biodb.DEBUG[2025-11-22 16:01:45.804][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)...
fscache.INFO [2025-11-22 16:01:45.807][cch$loadContents] Load 3 contents, from /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649.
biodb.DEBUG[2025-11-22 16:01:45.808][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-11-22 16:01:45.809][conn$getEntryContent] 3 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-11-22 16:01:45.810][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-11-22 16:01:45.811][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-11-22 16:01:45.817][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-11-22 16:01:45.818][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:01:45.819][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:01:45.823][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:01:45.824][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:01:45.825][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:01:45.826][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
sched.DEBUG[2025-11-22 16:01:45.827][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440".
fscache.INFO [2025-11-22 16:01:45.847][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched.
sched.DEBUG[2025-11-22 16:01:45.848][private$doSendRequestLoop] Request header is: "".
sched.DEBUG[2025-11-22 16:01:45.849][private$doSendRequestLoop] Request body is "".
sched.TRACE[2025-11-22 16:01:45.851][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440".
sched.TRACE[2025-11-22 16:01:46.841][does_rcurl_request_url_exist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440 does not exist.
sched.TRACE[2025-11-22 16:01:46.843][get_url_request_result] Using base::url() for sending request.
sched.DEBUG[2025-11-22 16:01:46.845][get_url_request_result] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
sched.TRACE[2025-11-22 16:01:46.848][get_base_url_request_result] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440).
sched.INFO [2025-11-22 16:01:47.640][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440". Retrying connection to server...
sched.DEBUG[2025-11-22 16:01:47.643][private$doSendRequestLoop] Request header is: "".
sched.DEBUG[2025-11-22 16:01:47.645][private$doSendRequestLoop] Request body is "".
sched.TRACE[2025-11-22 16:01:47.648][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440".
sched.TRACE[2025-11-22 16:01:48.003][does_rcurl_request_url_exist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440 does not exist.
sched.TRACE[2025-11-22 16:01:48.006][get_url_request_result] Using base::url() for sending request.
sched.DEBUG[2025-11-22 16:01:48.008][get_url_request_result] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
sched.TRACE[2025-11-22 16:01:48.010][get_base_url_request_result] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440).
sched.INFO [2025-11-22 16:01:48.785][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440". Retrying connection to server...
sched.DEBUG[2025-11-22 16:01:48.788][private$doSendRequestLoop] Request header is: "".
sched.DEBUG[2025-11-22 16:01:48.790][private$doSendRequestLoop] Request body is "".
sched.TRACE[2025-11-22 16:01:48.793][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440".
sched.TRACE[2025-11-22 16:01:49.148][does_rcurl_request_url_exist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440 does not exist.
sched.TRACE[2025-11-22 16:01:49.150][get_url_request_result] Using base::url() for sending request.
sched.DEBUG[2025-11-22 16:01:49.152][get_url_request_result] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
sched.TRACE[2025-11-22 16:01:49.155][get_base_url_request_result] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440).
sched.INFO [2025-11-22 16:01:49.624][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440". Retrying connection to server...
sched.DEBUG[2025-11-22 16:01:49.628][private$doSendRequestLoop] Request header is: "".
sched.DEBUG[2025-11-22 16:01:49.630][private$doSendRequestLoop] Request body is "".
sched.TRACE[2025-11-22 16:01:49.634][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440".
sched.TRACE[2025-11-22 16:01:49.987][does_rcurl_request_url_exist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440 does not exist.
sched.TRACE[2025-11-22 16:01:49.989][get_url_request_result] Using base::url() for sending request.
sched.DEBUG[2025-11-22 16:01:49.991][get_url_request_result] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
sched.TRACE[2025-11-22 16:01:49.994][get_base_url_request_result] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440).
sched.INFO [2025-11-22 16:01:50.453][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440". Retrying connection to server...
sched.DEBUG[2025-11-22 16:01:50.455][private$doSendRequestLoop] Request header is: "".
sched.DEBUG[2025-11-22 16:01:50.458][private$doSendRequestLoop] Request body is "".
sched.TRACE[2025-11-22 16:01:50.461][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440".
sched.TRACE[2025-11-22 16:01:50.818][does_rcurl_request_url_exist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440 does not exist.
sched.TRACE[2025-11-22 16:01:50.820][get_url_request_result] Using base::url() for sending request.
sched.DEBUG[2025-11-22 16:01:50.823][get_url_request_result] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
sched.TRACE[2025-11-22 16:01:50.826][get_base_url_request_result] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440).
sched.INFO [2025-11-22 16:01:51.294][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440". Retrying connection to server...
sched.DEBUG[2025-11-22 16:01:51.297][private$doSendRequestLoop] Request header is: "".
sched.DEBUG[2025-11-22 16:01:51.299][private$doSendRequestLoop] Request body is "".
sched.TRACE[2025-11-22 16:01:51.303][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440".
sched.TRACE[2025-11-22 16:01:51.663][does_rcurl_request_url_exist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440 does not exist.
sched.TRACE[2025-11-22 16:01:51.665][get_url_request_result] Using base::url() for sending request.
sched.DEBUG[2025-11-22 16:01:51.668][get_url_request_result] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
sched.TRACE[2025-11-22 16:01:51.671][get_base_url_request_result] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440).
sched.INFO [2025-11-22 16:01:52.129][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440". Retrying connection to server...
sched.DEBUG[2025-11-22 16:01:52.191][private$doSendRequestLoop] Request header is: "".
sched.DEBUG[2025-11-22 16:01:52.194][private$doSendRequestLoop] Request body is "".
sched.TRACE[2025-11-22 16:01:52.196][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440".
sched.TRACE[2025-11-22 16:01:52.546][does_rcurl_request_url_exist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440 does not exist.
sched.TRACE[2025-11-22 16:01:52.548][get_url_request_result] Using base::url() for sending request.
sched.DEBUG[2025-11-22 16:01:52.551][get_url_request_result] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
sched.TRACE[2025-11-22 16:01:52.553][get_base_url_request_result] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440).
sched.INFO [2025-11-22 16:01:53.021][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440". Retrying connection to server...
sched.DEBUG[2025-11-22 16:01:53.023][private$doSendRequestLoop] Request header is: "".
sched.DEBUG[2025-11-22 16:01:53.026][private$doSendRequestLoop] Request body is "".
sched.TRACE[2025-11-22 16:01:53.029][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440".
sched.TRACE[2025-11-22 16:01:53.388][does_rcurl_request_url_exist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440 does not exist.
sched.TRACE[2025-11-22 16:01:53.390][get_url_request_result] Using base::url() for sending request.
sched.DEBUG[2025-11-22 16:01:53.392][get_url_request_result] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
sched.TRACE[2025-11-22 16:01:53.394][get_base_url_request_result] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440).
sched.INFO [2025-11-22 16:01:53.853][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440". Retrying connection to server...
sched.DEBUG[2025-11-22 16:01:53.855][private$doSendRequestLoop] Request header is: "".
sched.DEBUG[2025-11-22 16:01:53.858][private$doSendRequestLoop] Request body is "".
sched.TRACE[2025-11-22 16:01:53.862][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440".
sched.TRACE[2025-11-22 16:01:54.221][does_rcurl_request_url_exist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440 does not exist.
sched.TRACE[2025-11-22 16:01:54.224][get_url_request_result] Using base::url() for sending request.
sched.DEBUG[2025-11-22 16:01:54.226][get_url_request_result] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
sched.TRACE[2025-11-22 16:01:54.229][get_base_url_request_result] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440).
sched.INFO [2025-11-22 16:01:54.697][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440". Retrying connection to server...
sched.DEBUG[2025-11-22 16:01:54.702][private$doSendRequestLoop] Request header is: "".
sched.DEBUG[2025-11-22 16:01:54.704][private$doSendRequestLoop] Request body is "".
sched.TRACE[2025-11-22 16:01:54.709][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440".
sched.TRACE[2025-11-22 16:01:55.065][does_rcurl_request_url_exist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440 does not exist.
sched.TRACE[2025-11-22 16:01:55.067][get_url_request_result] Using base::url() for sending request.
sched.DEBUG[2025-11-22 16:01:55.068][get_url_request_result] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
sched.TRACE[2025-11-22 16:01:55.070][get_base_url_request_result] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440).
sched.INFO [2025-11-22 16:01:55.530][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440". Retrying connection to server...
biodb.DEBUG[2025-11-22 16:01:55.537][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-11-22 16:01:55.540][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:01:55.543][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:01:55.561][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:01:55.563][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:01:55.566][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:01:55.568][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
sched.DEBUG[2025-11-22 16:01:55.602][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
fscache.INFO [2025-11-22 16:01:55.639][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched.
sched.DEBUG[2025-11-22 16:01:55.655][private$doSendRequestLoop] Request header is: "".
sched.DEBUG[2025-11-22 16:01:55.657][private$doSendRequestLoop] Request body is "".
sched.TRACE[2025-11-22 16:01:55.658][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
sched.TRACE[2025-11-22 16:01:56.003][does_rcurl_request_url_exist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528 does not exist.
sched.TRACE[2025-11-22 16:01:56.005][get_url_request_result] Using base::url() for sending request.
sched.DEBUG[2025-11-22 16:01:56.007][get_url_request_result] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
sched.TRACE[2025-11-22 16:01:56.009][get_base_url_request_result] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528).
sched.INFO [2025-11-22 16:01:56.467][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528". Retrying connection to server...
sched.DEBUG[2025-11-22 16:01:56.470][private$doSendRequestLoop] Request header is: "".
sched.DEBUG[2025-11-22 16:01:56.472][private$doSendRequestLoop] Request body is "".
sched.TRACE[2025-11-22 16:01:56.475][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
sched.TRACE[2025-11-22 16:01:56.833][does_rcurl_request_url_exist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528 does not exist.
sched.TRACE[2025-11-22 16:01:56.835][get_url_request_result] Using base::url() for sending request.
sched.DEBUG[2025-11-22 16:01:56.838][get_url_request_result] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
sched.TRACE[2025-11-22 16:01:56.840][get_base_url_request_result] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528).
sched.INFO [2025-11-22 16:01:57.298][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528". Retrying connection to server...
sched.DEBUG[2025-11-22 16:01:57.300][private$doSendRequestLoop] Request header is: "".
sched.DEBUG[2025-11-22 16:01:57.303][private$doSendRequestLoop] Request body is "".
sched.TRACE[2025-11-22 16:01:57.306][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
sched.TRACE[2025-11-22 16:01:57.666][does_rcurl_request_url_exist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528 does not exist.
sched.TRACE[2025-11-22 16:01:57.668][get_url_request_result] Using base::url() for sending request.
sched.DEBUG[2025-11-22 16:01:57.671][get_url_request_result] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
sched.TRACE[2025-11-22 16:01:57.673][get_base_url_request_result] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528).
sched.INFO [2025-11-22 16:01:58.143][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528". Retrying connection to server...
sched.DEBUG[2025-11-22 16:01:58.146][private$doSendRequestLoop] Request header is: "".
sched.DEBUG[2025-11-22 16:01:58.148][private$doSendRequestLoop] Request body is "".
sched.TRACE[2025-11-22 16:01:58.152][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
sched.TRACE[2025-11-22 16:01:58.549][does_rcurl_request_url_exist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528 does not exist.
sched.TRACE[2025-11-22 16:01:58.551][get_url_request_result] Using base::url() for sending request.
sched.DEBUG[2025-11-22 16:01:58.553][get_url_request_result] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
sched.TRACE[2025-11-22 16:01:58.556][get_base_url_request_result] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528).
sched.INFO [2025-11-22 16:01:59.022][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528". Retrying connection to server...
sched.DEBUG[2025-11-22 16:01:59.025][private$doSendRequestLoop] Request header is: "".
sched.DEBUG[2025-11-22 16:01:59.028][private$doSendRequestLoop] Request body is "".
sched.TRACE[2025-11-22 16:01:59.031][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
sched.TRACE[2025-11-22 16:01:59.391][does_rcurl_request_url_exist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528 does not exist.
sched.TRACE[2025-11-22 16:01:59.394][get_url_request_result] Using base::url() for sending request.
sched.DEBUG[2025-11-22 16:01:59.396][get_url_request_result] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
sched.TRACE[2025-11-22 16:01:59.399][get_base_url_request_result] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528).
sched.INFO [2025-11-22 16:01:59.868][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528". Retrying connection to server...
sched.DEBUG[2025-11-22 16:01:59.870][private$doSendRequestLoop] Request header is: "".
sched.DEBUG[2025-11-22 16:01:59.873][private$doSendRequestLoop] Request body is "".
sched.TRACE[2025-11-22 16:01:59.876][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
sched.TRACE[2025-11-22 16:02:00.233][does_rcurl_request_url_exist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528 does not exist.
sched.TRACE[2025-11-22 16:02:00.235][get_url_request_result] Using base::url() for sending request.
sched.DEBUG[2025-11-22 16:02:00.237][get_url_request_result] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
sched.TRACE[2025-11-22 16:02:00.239][get_base_url_request_result] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528).
sched.INFO [2025-11-22 16:02:00.699][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528". Retrying connection to server...
sched.DEBUG[2025-11-22 16:02:00.702][private$doSendRequestLoop] Request header is: "".
sched.DEBUG[2025-11-22 16:02:00.705][private$doSendRequestLoop] Request body is "".
sched.TRACE[2025-11-22 16:02:00.708][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
sched.TRACE[2025-11-22 16:02:01.057][does_rcurl_request_url_exist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528 does not exist.
sched.TRACE[2025-11-22 16:02:01.059][get_url_request_result] Using base::url() for sending request.
sched.DEBUG[2025-11-22 16:02:01.061][get_url_request_result] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
sched.TRACE[2025-11-22 16:02:01.064][get_base_url_request_result] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528).
sched.INFO [2025-11-22 16:02:01.535][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528". Retrying connection to server...
sched.DEBUG[2025-11-22 16:02:01.538][private$doSendRequestLoop] Request header is: "".
sched.DEBUG[2025-11-22 16:02:01.541][private$doSendRequestLoop] Request body is "".
sched.TRACE[2025-11-22 16:02:01.544][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
sched.TRACE[2025-11-22 16:02:01.891][does_rcurl_request_url_exist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528 does not exist.
sched.TRACE[2025-11-22 16:02:01.894][get_url_request_result] Using base::url() for sending request.
sched.DEBUG[2025-11-22 16:02:01.896][get_url_request_result] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
sched.TRACE[2025-11-22 16:02:01.898][get_base_url_request_result] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528).
sched.INFO [2025-11-22 16:02:02.500][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528". Retrying connection to server...
sched.DEBUG[2025-11-22 16:02:02.503][private$doSendRequestLoop] Request header is: "".
sched.DEBUG[2025-11-22 16:02:02.505][private$doSendRequestLoop] Request body is "".
sched.TRACE[2025-11-22 16:02:02.508][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
sched.TRACE[2025-11-22 16:02:02.865][does_rcurl_request_url_exist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528 does not exist.
sched.TRACE[2025-11-22 16:02:02.867][get_url_request_result] Using base::url() for sending request.
sched.DEBUG[2025-11-22 16:02:02.869][get_url_request_result] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
sched.TRACE[2025-11-22 16:02:02.871][get_base_url_request_result] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528).
sched.INFO [2025-11-22 16:02:03.341][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528". Retrying connection to server...
sched.DEBUG[2025-11-22 16:02:03.343][private$doSendRequestLoop] Request header is: "".
sched.DEBUG[2025-11-22 16:02:03.345][private$doSendRequestLoop] Request body is "".
sched.TRACE[2025-11-22 16:02:03.348][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
sched.TRACE[2025-11-22 16:02:03.713][does_rcurl_request_url_exist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528 does not exist.
sched.TRACE[2025-11-22 16:02:03.717][get_url_request_result] Using base::url() for sending request.
sched.DEBUG[2025-11-22 16:02:03.719][get_url_request_result] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
sched.TRACE[2025-11-22 16:02:03.722][get_base_url_request_result] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528).
sched.INFO [2025-11-22 16:02:04.181][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528". Retrying connection to server...
biodb.DEBUG[2025-11-22 16:02:04.185][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-11-22 16:02:04.187][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:02:04.190][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:02:04.204][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:02:04.207][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:02:04.209][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:04.212][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
sched.DEBUG[2025-11-22 16:02:04.214][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
fscache.INFO [2025-11-22 16:02:04.220][private$cache$loadContents] Load 1 contents, from /home/biocbuild/.cache/R/sched.
sched.DEBUG[2025-11-22 16:02:04.223][private$doSendRequestLoop] Request header is: "".
sched.DEBUG[2025-11-22 16:02:04.225][private$doSendRequestLoop] Request body is "".
sched.TRACE[2025-11-22 16:02:04.228][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
sched.TRACE[2025-11-22 16:02:04.577][does_rcurl_request_url_exist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799 does not exist.
sched.TRACE[2025-11-22 16:02:04.579][get_url_request_result] Using base::url() for sending request.
sched.DEBUG[2025-11-22 16:02:04.582][get_url_request_result] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
sched.TRACE[2025-11-22 16:02:04.584][get_base_url_request_result] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799).
sched.INFO [2025-11-22 16:02:05.047][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799". Retrying connection to server...
sched.DEBUG[2025-11-22 16:02:05.050][private$doSendRequestLoop] Request header is: "".
sched.DEBUG[2025-11-22 16:02:05.053][private$doSendRequestLoop] Request body is "".
sched.TRACE[2025-11-22 16:02:05.056][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
sched.TRACE[2025-11-22 16:02:05.411][does_rcurl_request_url_exist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799 does not exist.
sched.TRACE[2025-11-22 16:02:05.413][get_url_request_result] Using base::url() for sending request.
sched.DEBUG[2025-11-22 16:02:05.415][get_url_request_result] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
sched.TRACE[2025-11-22 16:02:05.418][get_base_url_request_result] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799).
sched.INFO [2025-11-22 16:02:05.878][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799". Retrying connection to server...
sched.DEBUG[2025-11-22 16:02:05.881][private$doSendRequestLoop] Request header is: "".
sched.DEBUG[2025-11-22 16:02:05.883][private$doSendRequestLoop] Request body is "".
sched.TRACE[2025-11-22 16:02:05.887][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
sched.TRACE[2025-11-22 16:02:06.248][does_rcurl_request_url_exist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799 does not exist.
sched.TRACE[2025-11-22 16:02:06.250][get_url_request_result] Using base::url() for sending request.
sched.DEBUG[2025-11-22 16:02:06.253][get_url_request_result] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
sched.TRACE[2025-11-22 16:02:06.255][get_base_url_request_result] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799).
sched.INFO [2025-11-22 16:02:06.716][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799". Retrying connection to server...
sched.DEBUG[2025-11-22 16:02:06.718][private$doSendRequestLoop] Request header is: "".
sched.DEBUG[2025-11-22 16:02:06.721][private$doSendRequestLoop] Request body is "".
sched.TRACE[2025-11-22 16:02:06.724][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
sched.TRACE[2025-11-22 16:02:07.076][does_rcurl_request_url_exist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799 does not exist.
sched.TRACE[2025-11-22 16:02:07.078][get_url_request_result] Using base::url() for sending request.
sched.DEBUG[2025-11-22 16:02:07.080][get_url_request_result] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
sched.TRACE[2025-11-22 16:02:07.083][get_base_url_request_result] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799).
sched.INFO [2025-11-22 16:02:07.554][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799". Retrying connection to server...
sched.DEBUG[2025-11-22 16:02:07.557][private$doSendRequestLoop] Request header is: "".
sched.DEBUG[2025-11-22 16:02:07.559][private$doSendRequestLoop] Request body is "".
sched.TRACE[2025-11-22 16:02:07.563][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
sched.TRACE[2025-11-22 16:02:07.914][does_rcurl_request_url_exist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799 does not exist.
sched.TRACE[2025-11-22 16:02:07.916][get_url_request_result] Using base::url() for sending request.
sched.DEBUG[2025-11-22 16:02:07.918][get_url_request_result] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
sched.TRACE[2025-11-22 16:02:07.921][get_base_url_request_result] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799).
sched.INFO [2025-11-22 16:02:08.392][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799". Retrying connection to server...
sched.DEBUG[2025-11-22 16:02:08.395][private$doSendRequestLoop] Request header is: "".
sched.DEBUG[2025-11-22 16:02:08.397][private$doSendRequestLoop] Request body is "".
sched.TRACE[2025-11-22 16:02:08.400][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
sched.TRACE[2025-11-22 16:02:08.759][does_rcurl_request_url_exist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799 does not exist.
sched.TRACE[2025-11-22 16:02:08.762][get_url_request_result] Using base::url() for sending request.
sched.DEBUG[2025-11-22 16:02:08.765][get_url_request_result] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
sched.TRACE[2025-11-22 16:02:08.767][get_base_url_request_result] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799).
sched.INFO [2025-11-22 16:02:09.234][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799". Retrying connection to server...
sched.DEBUG[2025-11-22 16:02:09.237][private$doSendRequestLoop] Request header is: "".
sched.DEBUG[2025-11-22 16:02:09.239][private$doSendRequestLoop] Request body is "".
sched.TRACE[2025-11-22 16:02:09.242][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
sched.TRACE[2025-11-22 16:02:09.600][does_rcurl_request_url_exist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799 does not exist.
sched.TRACE[2025-11-22 16:02:09.602][get_url_request_result] Using base::url() for sending request.
sched.DEBUG[2025-11-22 16:02:09.605][get_url_request_result] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
sched.TRACE[2025-11-22 16:02:09.607][get_base_url_request_result] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799).
sched.INFO [2025-11-22 16:02:10.208][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799". Retrying connection to server...
sched.DEBUG[2025-11-22 16:02:10.210][private$doSendRequestLoop] Request header is: "".
sched.DEBUG[2025-11-22 16:02:10.213][private$doSendRequestLoop] Request body is "".
sched.TRACE[2025-11-22 16:02:10.216][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
sched.TRACE[2025-11-22 16:02:10.574][does_rcurl_request_url_exist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799 does not exist.
sched.TRACE[2025-11-22 16:02:10.576][get_url_request_result] Using base::url() for sending request.
sched.DEBUG[2025-11-22 16:02:10.579][get_url_request_result] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
sched.TRACE[2025-11-22 16:02:10.581][get_base_url_request_result] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799).
sched.INFO [2025-11-22 16:02:11.043][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799". Retrying connection to server...
sched.DEBUG[2025-11-22 16:02:11.045][private$doSendRequestLoop] Request header is: "".
sched.DEBUG[2025-11-22 16:02:11.048][private$doSendRequestLoop] Request body is "".
sched.TRACE[2025-11-22 16:02:11.051][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
sched.TRACE[2025-11-22 16:02:11.415][does_rcurl_request_url_exist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799 does not exist.
sched.TRACE[2025-11-22 16:02:11.418][get_url_request_result] Using base::url() for sending request.
sched.DEBUG[2025-11-22 16:02:11.420][get_url_request_result] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
sched.TRACE[2025-11-22 16:02:11.421][get_base_url_request_result] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799).
sched.INFO [2025-11-22 16:02:11.888][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799". Retrying connection to server...
sched.DEBUG[2025-11-22 16:02:11.891][private$doSendRequestLoop] Request header is: "".
sched.DEBUG[2025-11-22 16:02:11.893][private$doSendRequestLoop] Request body is "".
sched.TRACE[2025-11-22 16:02:11.897][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
sched.TRACE[2025-11-22 16:02:12.255][does_rcurl_request_url_exist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799 does not exist.
sched.TRACE[2025-11-22 16:02:12.269][get_url_request_result] Using base::url() for sending request.
sched.DEBUG[2025-11-22 16:02:12.271][get_url_request_result] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
sched.TRACE[2025-11-22 16:02:12.273][get_base_url_request_result] Using base::url() for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799).
sched.INFO [2025-11-22 16:02:12.737][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799". Retrying connection to server...
fscache.INFO [2025-11-22 16:02:12.742][cch$saveContents] Save 3 contents to /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649.
biodb.DEBUG[2025-11-22 16:02:12.744][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-11-22 16:02:12.748][self$createEntryFromContent] Creating ChEBI entries from 3 content(s).
biodb.DEBUG[2025-11-22 16:02:12.751][self$createEntryFromContent] Parsing 3 ChEBI entries.
biodb.DEBUG[2025-11-22 16:02:12.755][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-11-22 16:02:12.757][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:02:12.759][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:02:12.770][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:02:12.773][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:02:12.775][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:12.777][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-11-22 16:02:12.781][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-22 16:02:12.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-22 16:02:12.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:12.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:12.790][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-22 16:02:12.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-22 16:02:12.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:12.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:12.797][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:12.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:12.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:12.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-11-22 16:02:12.803][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-11-22 16:02:12.805][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:02:12.806][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:02:12.812][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:02:12.813][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:02:12.814][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:12.815][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-11-22 16:02:12.818][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-22 16:02:12.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-22 16:02:12.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:12.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:12.822][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-22 16:02:12.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-22 16:02:12.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:12.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:12.826][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:12.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:12.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:12.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-11-22 16:02:12.831][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-11-22 16:02:12.831][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:02:12.832][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:02:12.836][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:02:12.837][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:02:12.838][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:12.839][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-11-22 16:02:12.841][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-22 16:02:12.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-22 16:02:12.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:12.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:12.845][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-11-22 16:02:12.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-11-22 16:02:12.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:12.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:12.848][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:12.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:12.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:12.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:12.852][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:12.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:12.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:12.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:12.856][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:12.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:12.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:12.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:12.860][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:12.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:12.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:12.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:12.864][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:12.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:12.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:12.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:12.868][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:12.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:12.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:12.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:12.872][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:12.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:12.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:12.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:12.876][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:12.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:12.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:12.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:12.880][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:12.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:12.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:12.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:12.883][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:12.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:12.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:12.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:12.887][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:12.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:12.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:12.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:12.891][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:12.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:12.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:12.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:12.895][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:12.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:12.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:12.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:12.899][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:12.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:12.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:12.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:12.902][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:12.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:12.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:12.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:12.906][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-11-22 16:02:12.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-11-22 16:02:12.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:12.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-11-22 16:02:12.910][self$createEntryFromContent] Accession numbers: NA, NA, NA.
biodb.DEBUG[2025-11-22 16:02:12.911][self$createEntryFromContent] Found 3 entry/ies without an accession number. Set it/them to NULL.
Saving _problems/test_long_100_generic-18.R
biodb.INFO [2025-11-22 16:02:13.043][biodb::testThat]
biodb.INFO [2025-11-22 16:02:13.045][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-11-22 16:02:13.046][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-22 16:02:13.046][biodb::testThat]
biodb.TRACE[2025-11-22 16:02:13.050][ef$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:02:13.051][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:02:13.052][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:13.052][ef$get] fields variable is a list.
biodb.DEBUG[2025-11-22 16:02:13.054][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name".
Saving _problems/test_long_100_generic-18.R
Saving _problems/test_long_100_generic-18.R
biodb.INFO [2025-11-22 16:02:13.279][biodb::testThat]
biodb.INFO [2025-11-22 16:02:13.281][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-11-22 16:02:13.281][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-22 16:02:13.282][biodb::testThat]
Saving _problems/test_long_100_generic-18.R
Saving _problems/test_long_100_generic-18.R
biodb.INFO [2025-11-22 16:02:13.377][biodb::testThat]
biodb.INFO [2025-11-22 16:02:13.378][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-11-22 16:02:13.379][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-22 16:02:13.383][biodb::testThat]
Saving _problems/test_long_100_generic-18.R
Saving _problems/test_long_100_generic-18.R
biodb.INFO [2025-11-22 16:02:13.478][biodb::testThat]
biodb.INFO [2025-11-22 16:02:13.479][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-11-22 16:02:13.480][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-22 16:02:13.481][biodb::testThat]
biodb.INFO [2025-11-22 16:02:13.489][biodb::testThat]
biodb.INFO [2025-11-22 16:02:13.490][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-11-22 16:02:13.491][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-22 16:02:13.492][biodb::testThat]
biodb.INFO [2025-11-22 16:02:13.498][biodb::testThat]
biodb.INFO [2025-11-22 16:02:13.499][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-11-22 16:02:13.500][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-22 16:02:13.501][biodb::testThat]
biodb.DEBUG[2025-11-22 16:02:13.504][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440".
sched.TRACE[2025-11-22 16:02:14.036][try_get_rcurl_content] Using RCurl package for sending request (https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440).
biodb.INFO [2025-11-22 16:02:14.409][biodb::testThat]
biodb.INFO [2025-11-22 16:02:14.412][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-11-22 16:02:14.414][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-22 16:02:14.416][biodb::testThat]
biodb.TRACE[2025-11-22 16:02:14.449][ef$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:02:14.451][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:02:14.452][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.454][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.455][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:02:14.456][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:02:14.457][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.459][ef$get] fields variable is a list.
biodb.INFO [2025-11-22 16:02:14.461][biodb::testThat]
biodb.INFO [2025-11-22 16:02:14.462][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2025-11-22 16:02:14.463][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-22 16:02:14.464][biodb::testThat]
Saving _problems/test_long_100_generic-18.R
Saving _problems/test_long_100_generic-18.R
biodb.INFO [2025-11-22 16:02:14.581][biodb::testThat]
biodb.INFO [2025-11-22 16:02:14.586][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2025-11-22 16:02:14.587][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-22 16:02:14.588][biodb::testThat]
Saving _problems/test_long_100_generic-18.R
biodb.INFO [2025-11-22 16:02:14.627][biodb::testThat]
biodb.INFO [2025-11-22 16:02:14.628][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2025-11-22 16:02:14.629][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-22 16:02:14.630][biodb::testThat]
Saving _problems/test_long_100_generic-18.R
biodb.INFO [2025-11-22 16:02:14.674][biodb::testThat]
biodb.INFO [2025-11-22 16:02:14.675][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2025-11-22 16:02:14.676][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-22 16:02:14.677][biodb::testThat]
Saving _problems/test_long_100_generic-18.R
biodb.TRACE[2025-11-22 16:02:14.718][ef$get] Asked field names are: name.
biodb.TRACE[2025-11-22 16:02:14.719][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-11-22 16:02:14.720][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.721][ef$get] fields variable is a list.
biodb.TRACE[2025-11-22 16:02:14.722][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:02:14.723][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-11-22 16:02:14.724][ef$get] 1 fields were returned.
biodb.TRACE[2025-11-22 16:02:14.725][ef$get] fields variable is a list.
biodb.INFO [2025-11-22 16:02:14.726][biodb::testThat]
biodb.INFO [2025-11-22 16:02:14.727][biodb::testThat] Running test function  test.annotateMzValues_real_values  (" annotateMzValues() works correctly with real values. ").
biodb.INFO [2025-11-22 16:02:14.728][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-22 16:02:14.729][biodb::testThat]
Saving _problems/test_long_100_generic-18.R
biodb.INFO [2025-11-22 16:02:14.775][biodb::testThat]
biodb.INFO [2025-11-22 16:02:14.776][biodb::testThat] Running test function  test_annotateMzValues_additional_fields  (" Additional fields are accepted in annotateMzValues() ").
biodb.INFO [2025-11-22 16:02:14.777][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-11-22 16:02:14.778][biodb::testThat]
Saving _problems/test_long_100_generic-18.R
biodb.INFO [2025-11-22 16:02:14.818][biodb$terminate] Closing BiodbMain instance...
biodb.INFO [2025-11-22 16:02:14.819][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-11-22 16:02:14.820][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-11-22 16:02:14.821][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-11-22 16:02:14.822][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-11-22 16:02:14.823][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-11-22 16:02:14.824][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-11-22 16:02:14.825][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-11-22 16:02:14.826][FUN] Functions in observer 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 14 | WARN 0 | SKIP 1 | PASS 220 ]

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

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_long_100_generic.R:17:1'): RT unit is defined when there is an RT value. ──
Error in `eval_bare(expr, quo_get_env(quo))`: attempt to apply non-function
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<ChebiCnn>`, opt = `<named list>`)
 3.   └─testthat::expect_true(...)
 4.     └─testthat::quasi_label(enquo(object), label)
 5.       └─rlang::eval_bare(expr, quo_get_env(quo))
── Failure ('test_long_100_generic.R:17:1'): We can search for an entry by searchable field ──
Expected `!is.null(entry)` to be TRUE.
Differences:
`actual`:   FALSE
`expected`: TRUE 

Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<ChebiCnn>`, opt = `<named list>`)
 3.   └─testthat::expect_true(!is.null(entry))
── Error ('test_long_100_generic.R:17:1'): We can search for an entry by searchable field ──
Error in `entry$getFieldValue(f)`: attempt to apply non-function
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<ChebiCnn>`, opt = `<named list>`)
── Failure ('test_long_100_generic.R:17:1'): We can search for an entry by name. ──
Expected `!is.null(entry)` to be TRUE.
Differences:
`actual`:   FALSE
`expected`: TRUE 

Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<ChebiCnn>`, opt = `<named list>`)
 3.   └─testthat::expect_true(!is.null(entry))
── Error ('test_long_100_generic.R:17:1'): We can search for an entry by name. ──
Error in `entry$getFieldValue("name")`: attempt to apply non-function
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<ChebiCnn>`, opt = `<named list>`)
── Failure ('test_long_100_generic.R:17:1'): We can load an entry from the database. ──
Expected `any(vapply(entries, is.null, FUN.VALUE = TRUE))` to be FALSE.
Differences:
`actual`:   TRUE 
`expected`: FALSE

Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<ChebiCnn>`, opt = `<named list>`)
 3.   └─opt$refEntries$getRealEntry(id)
 4.     └─self$getRealEntries(ids = id)
 5.       └─testthat::expect_false(any(vapply(entries, is.null, FUN.VALUE = TRUE)))
── Failure ('test_long_100_generic.R:17:1'): We can load an entry from the database. ──
Expected `e` to inherit from "character".
Actual inheritance: "NULL"
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<ChebiCnn>`, opt = `<named list>`)
 3.   └─testthat::expect_is(e, "BiodbEntry")
── Failure ('test_long_100_generic.R:17:1'): We can search for a compound ──────
Expected `!is.null(entry)` to be TRUE.
Differences:
`actual`:   FALSE
`expected`: TRUE 

Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(db = `<ChebiCnn>`, opt = `<named list>`)
 3.   └─testthat::expect_true(!is.null(entry))
── Error ('test_long_100_generic.R:17:1'): We can search for a compound ────────
Error in `entry$getFieldValue("name")`: attempt to apply non-function
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(db = `<ChebiCnn>`, opt = `<named list>`)
── Error ('test_long_100_generic.R:17:1'): annotateMzValues() accepts a single vector. ──
Error in `e$hasField(mf)`: attempt to apply non-function
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<ChebiCnn>`, opt = `<named list>`)
 3.   └─base::vapply(entries, function(e) e$hasField(mf), FUN.VALUE = TRUE)
 4.     └─biodb (local) FUN(X[[i]], ...)
── Error ('test_long_100_generic.R:17:1'): ppm tolerance works in annotateMzValues() ──
Error in `e$hasField(mf)`: attempt to apply non-function
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<ChebiCnn>`, opt = `<named list>`)
 3.   └─base::vapply(entries, function(e) e$hasField(mf), FUN.VALUE = TRUE)
 4.     └─biodb (local) FUN(X[[i]], ...)
── Error ('test_long_100_generic.R:17:1'): Input data frame is not modified by annotateMzValues() ──
Error in `e$hasField(mf)`: attempt to apply non-function
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<ChebiCnn>`, opt = `<named list>`)
 3.   └─base::vapply(entries, function(e) e$hasField(mf), FUN.VALUE = TRUE)
 4.     └─biodb (local) FUN(X[[i]], ...)
── Error ('test_long_100_generic.R:17:1'): annotateMzValues() works correctly with real values. ──
Error in `e$hasField(mf)`: attempt to apply non-function
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<ChebiCnn>`, opt = `<named list>`)
 3.   └─base::vapply(entries, function(e) e$hasField(mf), FUN.VALUE = TRUE)
 4.     └─biodb (local) FUN(X[[i]], ...)
── Error ('test_long_100_generic.R:17:1'): Additional fields are accepted in annotateMzValues() ──
Error in `e$hasField(mf)`: attempt to apply non-function
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<ChebiCnn>`, opt = `<named list>`)
 3.   └─base::vapply(entries, function(e) e$hasField(mf), FUN.VALUE = TRUE)
 4.     └─biodb (local) FUN(X[[i]], ...)

[ FAIL 14 | WARN 0 | SKIP 1 | PASS 220 ]
Error:
! Test failures.
Execution halted

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.23-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 biodbChebi_1.17.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.23-bioc-longtests/meat/biodbChebi.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘biodbChebi/DESCRIPTION’ ... OK
* this is package ‘biodbChebi’ version ‘1.17.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbChebi’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... SKIPPED
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... 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:
   3.   └─base::vapply(entries, function(e) e$hasField(mf), FUN.VALUE = TRUE)
   4.     └─biodb (local) FUN(X[[i]], ...)
  ── Error ('test_long_100_generic.R:17:1'): Additional fields are accepted in annotateMzValues() ──
  Error in `e$hasField(mf)`: attempt to apply non-function
  Backtrace:
      ▆
   1. ├─base::do.call(fct, params)
   2. └─biodb (local) `<fn>`(conn = `<ChebiCnn>`, opt = `<named list>`)
   3.   └─base::vapply(entries, function(e) e$hasField(mf), FUN.VALUE = TRUE)
   4.     └─biodb (local) FUN(X[[i]], ...)
  
  [ FAIL 14 | WARN 0 | SKIP 1 | PASS 220 ]
  Error:
  ! Test failures.
  Execution halted
* DONE

Status: 1 ERROR
See
  ‘/home/biocbuild/bbs-3.23-bioc-longtests/meat/biodbChebi.Rcheck/00check.log’
for details.

Installation output

biodbChebi.Rcheck/00install.out

* installing *source* package ‘biodbChebi’ ...
** this is package ‘biodbChebi’ version ‘1.17.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (biodbChebi)