Back to Long Tests report for BioC 3.21

This page was generated on 2025-04-19 23:55 -0400 (Sat, 19 Apr 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4831
palomino7Windows Server 2022 Datacenterx644.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six" 4573
lconwaymacOS 12.7.1 Montereyx86_644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4599
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 7/30HostnameOS / ArchCHECK
biodbHmdb 1.14.0  (landing page)
Pierrick Roger
Snapshot Date: 2025-04-19 09:55 -0400 (Sat, 19 Apr 2025)
git_url: https://git.bioconductor.org/packages/biodbHmdb
git_branch: RELEASE_3_21
git_last_commit: a7f0a0f
git_last_commit_date: 2025-04-15 12:42:50 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  WARNINGS  
palomino7Windows Server 2022 Datacenter / x64  ERROR  
lconwaymacOS 12.7.1 Monterey / x86_64  WARNINGS  

CHECK results for biodbHmdb on palomino7

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

raw results


Summary

Package: biodbHmdb
Version: 1.14.0
Command: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbHmdb_1.14.0.tar.gz
StartedAt: 2025-04-19 16:03:46 -0400 (Sat, 19 Apr 2025)
EndedAt: 2025-04-19 16:05:25 -0400 (Sat, 19 Apr 2025)
EllapsedTime: 98.3 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbHmdb.Rcheck
Warnings: NA

Tests output

biodbHmdb.Rcheck/tests/testthat.Rout.fail


R version 4.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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

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

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

> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbHmdb)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbHmdb")
biodb.INFO [2025-04-19 16:05:17.824][biodb::testContext]
biodb.INFO [2025-04-19 16:05:17.827][biodb::testContext] ********************************************************************************
biodb.INFO [2025-04-19 16:05:17.829][biodb::testContext] Test context - Generic long tests
biodb.INFO [2025-04-19 16:05:17.830][biodb::testContext] ********************************************************************************
biodb.INFO [2025-04-19 16:05:17.831][biodb::testContext]
biodb.INFO [2025-04-19 16:05:17.837][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.16.0.
biodb.DEBUG[2025-04-19 16:05:17.840][self$loadDefinitions] Load definitions from file "E:/biocbuild/bbs-3.21-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2025-04-19 16:05:17.849][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-19 16:05:17.851][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-04-19 16:05:17.853][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-04-19 16:05:17.854][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:05:17.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:05:17.856][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:05:17.857][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-04-19 16:05:17.873][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-04-19 16:05:17.875][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:05:17.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:05:17.877][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:05:17.878][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-04-19 16:05:17.879][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-04-19 16:05:17.880][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:05:17.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:05:17.882][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:05:17.884][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-04-19 16:05:17.885][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-04-19 16:05:17.886][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-04-19 16:05:17.887][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:05:17.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:05:17.889][FUN] Functions in observer BiodbConfig: [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[2025-04-19 16:05:17.890][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-04-19 16:05:17.892][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-04-19 16:05:17.893][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-04-19 16:05:17.894][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:05:17.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:05:17.896][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:05:17.897][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-04-19 16:05:17.898][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-04-19 16:05:17.899][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:05:17.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:05:17.901][FUN] Functions in observer BiodbConfig: [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[2025-04-19 16:05:17.903][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-04-19 16:05:17.904][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-04-19 16:05:17.906][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-04-19 16:05:17.907][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:05:17.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:05:17.910][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:05:17.912][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-04-19 16:05:17.914][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-04-19 16:05:17.916][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:05:17.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:05:17.919][FUN] Functions in observer BiodbConfig: [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[2025-04-19 16:05:17.920][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-04-19 16:05:17.922][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-04-19 16:05:17.924][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-04-19 16:05:17.925][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:05:17.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:05:17.927][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:05:17.929][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-04-19 16:05:17.930][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-04-19 16:05:17.931][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-04-19 16:05:17.932][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-04-19 16:05:17.933][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-04-19 16:05:17.935][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-04-19 16:05:17.936][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:05:17.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:05:17.938][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[2025-04-19 16:05:17.939][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-04-19 16:05:17.940][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-04-19 16:05:17.941][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:05:17.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:05:17.943][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:05:17.945][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-04-19 16:05:17.946][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-04-19 16:05:17.947][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:05:17.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:05:17.949][FUN] Functions in observer BiodbConfig: [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[2025-04-19 16:05:17.950][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-04-19 16:05:17.951][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-04-19 16:05:17.952][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:05:17.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:05:17.954][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:05:17.956][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-04-19 16:05:17.957][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-04-19 16:05:17.958][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:05:17.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:05:17.960][FUN] Functions in observer BiodbConfig: [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[2025-04-19 16:05:17.961][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-04-19 16:05:17.962][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-04-19 16:05:17.963][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:05:17.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:05:17.966][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:05:17.967][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-04-19 16:05:17.968][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-04-19 16:05:17.971][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-04-19 16:05:17.972][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:05:17.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:05:17.974][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[2025-04-19 16:05:17.975][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-04-19 16:05:17.977][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-04-19 16:05:17.978][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-04-19 16:05:17.979][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:05:17.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:05:17.981][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:05:17.984][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-04-19 16:05:18.011][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-19 16:05:18.032][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-04-19 16:05:18.033][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-19 16:05:18.035][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-19 16:05:18.036][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-19 16:05:18.037][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-19 16:05:18.038][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-19 16:05:18.039][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-19 16:05:18.040][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-04-19 16:05:18.042][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-19 16:05:18.043][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-19 16:05:18.044][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-04-19 16:05:18.045][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-19 16:05:18.046][self$setPropertyValue]
biodb.DEBUG[2025-04-19 16:05:18.048][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-19 16:05:18.049][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-19 16:05:18.049][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-19 16:05:18.049][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-19 16:05:18.049][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-04-19 16:05:18.049][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-04-19 16:05:18.050][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-19 16:05:18.051][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-19 16:05:18.052][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-19 16:05:18.054][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-19 16:05:18.055][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-19 16:05:18.056][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-19 16:05:18.057][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-19 16:05:18.058][self$setPropertyValue]
biodb.DEBUG[2025-04-19 16:05:18.059][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-19 16:05:18.060][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-19 16:05:18.062][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-19 16:05:18.063][self$setPropertyValue]
biodb.DEBUG[2025-04-19 16:05:18.064][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-04-19 16:05:18.066][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-19 16:05:18.067][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-04-19 16:05:18.069][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-19 16:05:18.070][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-19 16:05:18.071][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-19 16:05:18.072][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-19 16:05:18.073][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-19 16:05:18.074][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-19 16:05:18.076][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-04-19 16:05:18.077][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-19 16:05:18.078][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-19 16:05:18.079][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-04-19 16:05:18.080][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-19 16:05:18.082][self$setPropertyValue]
biodb.DEBUG[2025-04-19 16:05:18.083][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-19 16:05:18.084][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-19 16:05:18.084][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-04-19 16:05:18.084][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-04-19 16:05:18.084][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-04-19 16:05:18.084][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-04-19 16:05:18.085][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-19 16:05:18.086][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-19 16:05:18.087][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-19 16:05:18.089][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-19 16:05:18.090][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-19 16:05:18.091][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-19 16:05:18.092][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-19 16:05:18.093][self$setPropertyValue]
biodb.DEBUG[2025-04-19 16:05:18.094][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-19 16:05:18.095][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-19 16:05:18.097][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-19 16:05:18.098][self$setPropertyValue]
biodb.DEBUG[2025-04-19 16:05:18.099][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-04-19 16:05:18.101][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-04-19 16:05:18.102][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-04-19 16:05:18.103][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-19 16:05:18.105][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-19 16:05:18.106][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-19 16:05:18.107][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-19 16:05:18.108][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-19 16:05:18.109][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-19 16:05:18.110][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-04-19 16:05:18.112][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-19 16:05:18.113][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-04-19 16:05:18.114][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-04-19 16:05:18.115][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-19 16:05:18.116][self$setPropertyValue]
biodb.DEBUG[2025-04-19 16:05:18.118][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-19 16:05:18.119][self$setPropertyValue]
biodb.DEBUG[2025-04-19 16:05:18.120][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-19 16:05:18.121][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-19 16:05:18.122][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-19 16:05:18.123][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-19 16:05:18.125][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-19 16:05:18.126][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-19 16:05:18.127][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-19 16:05:18.128][self$setPropertyValue]
biodb.DEBUG[2025-04-19 16:05:18.129][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-19 16:05:18.130][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-19 16:05:18.131][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-19 16:05:18.133][self$setPropertyValue]
biodb.DEBUG[2025-04-19 16:05:18.134][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-04-19 16:05:18.136][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-04-19 16:05:18.137][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-04-19 16:05:18.138][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-19 16:05:18.139][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-19 16:05:18.140][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-04-19 16:05:18.142][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-04-19 16:05:18.143][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-04-19 16:05:18.144][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-19 16:05:18.145][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-04-19 16:05:18.147][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-19 16:05:18.148][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-04-19 16:05:18.149][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-04-19 16:05:18.150][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-19 16:05:18.151][self$setPropertyValue]
biodb.DEBUG[2025-04-19 16:05:18.153][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-04-19 16:05:18.154][self$setPropertyValue]
biodb.DEBUG[2025-04-19 16:05:18.155][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-04-19 16:05:18.156][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-19 16:05:18.157][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-19 16:05:18.158][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-19 16:05:18.159][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-19 16:05:18.161][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-19 16:05:18.162][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-19 16:05:18.163][self$setPropertyValue]
biodb.DEBUG[2025-04-19 16:05:18.164][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-19 16:05:18.165][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-19 16:05:18.166][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-04-19 16:05:18.167][self$setPropertyValue]
biodb.DEBUG[2025-04-19 16:05:18.171][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-19 16:05:18.172][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:05:18.173][FUN] Functions in observer BiodbConfig: [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[2025-04-19 16:05:18.174][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:05:18.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:05:18.176][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:05:18.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:05:18.178][FUN] Functions in observer BiodbConfig: [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[2025-04-19 16:05:18.180][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:05:18.181][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:05:18.182][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:05:18.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:05:18.184][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[2025-04-19 16:05:18.185][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:05:18.186][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:05:18.187][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:05:18.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:05:18.189][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[2025-04-19 16:05:18.190][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:05:18.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:05:18.193][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:05:18.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:05:18.195][FUN] Functions in observer BiodbConfig: [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[2025-04-19 16:05:18.196][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:05:18.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:05:18.198][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:05:18.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:05:18.200][FUN] Functions in observer BiodbConfig: [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[2025-04-19 16:05:18.201][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:05:18.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:05:18.203][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:05:18.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:05:18.206][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[2025-04-19 16:05:18.207][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:05:18.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:05:18.209][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:05:18.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:05:18.211][FUN] Functions in observer BiodbConfig: [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[2025-04-19 16:05:18.212][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:05:18.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:05:18.214][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:05:18.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:05:18.216][FUN] Functions in observer BiodbConfig: [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[2025-04-19 16:05:18.217][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:05:18.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:05:18.219][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:05:18.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:05:18.222][FUN] Functions in observer BiodbConfig: [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[2025-04-19 16:05:18.223][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:05:18.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:05:18.225][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:05:18.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:05:18.227][FUN] Functions in observer BiodbConfig: [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[2025-04-19 16:05:18.228][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:05:18.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:05:18.230][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:05:18.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:05:18.232][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:05:18.233][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:05:18.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:05:18.236][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:05:18.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:05:18.238][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[2025-04-19 16:05:18.239][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:05:18.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:05:18.241][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:05:18.242][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:05:18.243][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[2025-04-19 16:05:18.245][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:05:18.246][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:05:18.251][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:05:18.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:05:18.254][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:05:18.255][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:05:18.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:05:18.257][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:05:18.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:05:18.259][FUN] Functions in observer BiodbConfig: [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[2025-04-19 16:05:18.260][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:05:18.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:05:18.262][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:05:18.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:05:18.264][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:05:18.265][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:05:18.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:05:18.268][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:05:18.269][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:05:18.270][FUN] Functions in observer BiodbConfig: [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[2025-04-19 16:05:18.271][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-04-19 16:05:18.275][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-04-19 16:05:18.277][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-04-19 16:05:18.278][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-04-19 16:05:18.280][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-04-19 16:05:18.282][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-04-19 16:05:18.283][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-04-19 16:05:18.285][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-04-19 16:05:18.286][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-04-19 16:05:18.288][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-04-19 16:05:18.289][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-04-19 16:05:18.291][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-04-19 16:05:18.293][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-04-19 16:05:18.294][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-04-19 16:05:18.296][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-04-19 16:05:18.297][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-04-19 16:05:18.299][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-04-19 16:05:18.300][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-04-19 16:05:18.302][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-04-19 16:05:18.303][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-04-19 16:05:18.305][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-04-19 16:05:18.307][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-04-19 16:05:18.308][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-04-19 16:05:18.310][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-04-19 16:05:18.311][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-04-19 16:05:18.313][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-04-19 16:05:18.314][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-04-19 16:05:18.316][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-04-19 16:05:18.318][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-04-19 16:05:18.319][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-04-19 16:05:18.321][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-04-19 16:05:18.322][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-04-19 16:05:18.324][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-04-19 16:05:18.325][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-04-19 16:05:18.327][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-04-19 16:05:18.328][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-04-19 16:05:18.330][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-04-19 16:05:18.332][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-04-19 16:05:18.333][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-04-19 16:05:18.335][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-04-19 16:05:18.336][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-04-19 16:05:18.338][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-04-19 16:05:18.339][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-04-19 16:05:18.341][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-04-19 16:05:18.342][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-04-19 16:05:18.344][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-04-19 16:05:18.345][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-04-19 16:05:18.347][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-04-19 16:05:18.349][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-04-19 16:05:18.350][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-04-19 16:05:18.352][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-04-19 16:05:18.353][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-04-19 16:05:18.355][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-04-19 16:05:18.356][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-04-19 16:05:18.358][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-04-19 16:05:18.359][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-04-19 16:05:18.361][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-04-19 16:05:18.362][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-04-19 16:05:18.364][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-04-19 16:05:18.365][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-04-19 16:05:18.367][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-04-19 16:05:18.368][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-04-19 16:05:18.370][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-04-19 16:05:18.372][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-04-19 16:05:18.373][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-04-19 16:05:18.375][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-04-19 16:05:18.376][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-04-19 16:05:18.378][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-04-19 16:05:18.379][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-04-19 16:05:18.381][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-04-19 16:05:18.382][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-04-19 16:05:18.384][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-04-19 16:05:18.385][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-04-19 16:05:18.387][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-04-19 16:05:18.388][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-04-19 16:05:18.390][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-04-19 16:05:18.392][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-04-19 16:05:18.393][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-04-19 16:05:18.395][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-04-19 16:05:18.396][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-04-19 16:05:18.398][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-04-19 16:05:18.399][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-04-19 16:05:18.401][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-04-19 16:05:18.426][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-04-19 16:05:18.428][initialize] This is biodb version 1.16.0.
biodb.DEBUG[2025-04-19 16:05:18.431][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-04-19 16:05:18.433][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:05:18.434][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:05:18.435][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:05:18.436][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[2025-04-19 16:05:18.440][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:05:18.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-19 16:05:18.442][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-19 16:05:18.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:05:18.444][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:05:18.445][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:05:18.447][FUN] Functions in observer BiodbConfig: [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[2025-04-19 16:05:18.448][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:05:18.449][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-19 16:05:18.450][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-19 16:05:18.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:05:18.452][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:05:18.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:05:18.454][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[2025-04-19 16:05:18.455][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:05:18.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-19 16:05:18.457][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-19 16:05:18.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:05:18.459][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:05:18.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:05:18.461][FUN] Functions in observer BiodbConfig: [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[2025-04-19 16:05:18.462][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:05:18.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-19 16:05:18.464][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-19 16:05:18.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:05:18.467][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:05:18.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:05:18.496][FUN] Functions in observer BiodbConfig: [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[2025-04-19 16:05:18.497][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:05:18.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-19 16:05:18.499][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-19 16:05:18.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:05:18.501][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:05:18.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:05:18.503][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[2025-04-19 16:05:18.504][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:05:18.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-19 16:05:18.507][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-19 16:05:18.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:05:18.509][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:05:18.510][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:05:18.511][FUN] Functions in observer BiodbConfig: [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[2025-04-19 16:05:18.512][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:05:18.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-19 16:05:18.514][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-19 16:05:18.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:05:18.516][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:05:18.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:05:18.518][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:05:18.519][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:05:18.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-19 16:05:18.521][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-19 16:05:18.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:05:18.523][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:05:18.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:05:18.525][FUN] Functions in observer BiodbConfig: [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[2025-04-19 16:05:18.527][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:05:18.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-19 16:05:18.529][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-19 16:05:18.530][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:05:18.531][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:05:18.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:05:18.533][FUN] Functions in observer BiodbConfig: [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[2025-04-19 16:05:18.534][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:05:18.535][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-19 16:05:18.536][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-19 16:05:18.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:05:18.538][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:05:18.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:05:18.541][FUN] Functions in observer BiodbConfig: [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[2025-04-19 16:05:18.542][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:05:18.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-19 16:05:18.544][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-19 16:05:18.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:05:18.546][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:05:18.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:05:18.548][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:05:18.549][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:05:18.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-19 16:05:18.551][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-19 16:05:18.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:05:18.553][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:05:18.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:05:18.555][FUN] Functions in observer BiodbConfig: [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[2025-04-19 16:05:18.557][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:05:18.558][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-19 16:05:18.559][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-19 16:05:18.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:05:18.561][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:05:18.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:05:18.563][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:05:18.564][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:05:18.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-19 16:05:18.566][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-19 16:05:18.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:05:18.568][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:05:18.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:05:18.570][FUN] Functions in observer BiodbConfig: [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[2025-04-19 16:05:18.571][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:05:18.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-19 16:05:18.574][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-19 16:05:18.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:05:18.576][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:05:18.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:05:18.578][FUN] Functions in observer BiodbConfig: [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[2025-04-19 16:05:18.579][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:05:18.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-19 16:05:18.581][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-19 16:05:18.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:05:18.583][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:05:18.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:05:18.585][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:05:18.586][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:05:18.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-19 16:05:18.589][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-19 16:05:18.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:05:18.591][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:05:18.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:05:18.593][FUN] Functions in observer BiodbConfig: [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[2025-04-19 16:05:18.594][biodb$getConfig()$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-04-19 16:05:18.595][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-04-19 16:05:18.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-19 16:05:18.597][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-19 16:05:18.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:05:18.599][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:05:18.600][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:05:18.601][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-04-19 16:05:18.605][biodb$loadDefinitions] Load definitions from file "E:/biocbuild/bbs-3.21-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/definitions.yml".
biodb.DEBUG[2025-04-19 16:05:18.613][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2025-04-19 16:05:18.615][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-04-19 16:05:18.617][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-04-19 16:05:18.618][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-04-19 16:05:18.619][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-04-19 16:05:18.620][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-04-19 16:05:18.621][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2025-04-19 16:05:18.622][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-04-19 16:05:18.624][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-04-19 16:05:18.625][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-04-19 16:05:18.626][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-04-19 16:05:18.627][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-04-19 16:05:18.628][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2025-04-19 16:05:18.630][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-04-19 16:05:18.631][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2025-04-19 16:05:18.631][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2025-04-19 16:05:18.631][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2025-04-19 16:05:18.631][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2025-04-19 16:05:18.631][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2025-04-19 16:05:18.631][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2025-04-19 16:05:18.631][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2025-04-19 16:05:18.631][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2025-04-19 16:05:18.631][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2025-04-19 16:05:18.631][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2025-04-19 16:05:18.631][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2025-04-19 16:05:18.631][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2025-04-19 16:05:18.631][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2025-04-19 16:05:18.631][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2025-04-19 16:05:18.631][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2025-04-19 16:05:18.631][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2025-04-19 16:05:18.631][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2025-04-19 16:05:18.631][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2025-04-19 16:05:18.632][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-04-19 16:05:18.633][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-04-19 16:05:18.633][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2025-04-19 16:05:18.633][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2025-04-19 16:05:18.635][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-04-19 16:05:18.636][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-19 16:05:18.637][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-19 16:05:18.638][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-04-19 16:05:18.639][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-04-19 16:05:18.640][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-04-19 16:05:18.641][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-04-19 16:05:18.643][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2025-04-19 16:05:18.643][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2025-04-19 16:05:18.644][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-04-19 16:05:18.645][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-04-19 16:05:18.646][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-04-19 16:05:18.647][self$setPropertyValue]
biodb.DEBUG[2025-04-19 16:05:18.652][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2025-04-19 16:05:18.654][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-04-19 16:05:18.656][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-04-19 16:05:18.658][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-04-19 16:05:18.659][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-04-19 16:05:18.680][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2025-04-19 16:05:18.682][initialize] Register connector hmdb.metabolites with the request scheduler
biodb.DEBUG[2025-04-19 16:05:18.685][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites.
biodb.DEBUG[2025-04-19 16:05:18.689][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2025-04-19 16:05:18.694][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-04-19 16:05:18.695][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-04-19 16:05:18.698][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca".
biodb.DEBUG[2025-04-19 16:05:18.699][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.INFO [2025-04-19 16:05:18.717][biodb::testThat]
biodb.INFO [2025-04-19 16:05:18.718][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-04-19 16:05:18.719][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-19 16:05:18.720][biodb::testThat]
biodb.TRACE[2025-04-19 16:05:18.726][loadFileContents] Loaded 1 files from cache: [1]: "E:/biocbuild/bbs-3.21-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/testref/entry-hmdb.metabolites-HMDB0000001-content.xml".
biodb.DEBUG[2025-04-19 16:05:18.728][biodb$getFactory()$createEntryFromCo ...] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-04-19 16:05:18.732][biodb$getFactory()$createEntryFromCo ...] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-04-19 16:05:18.739][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-04-19 16:05:18.740][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-19 16:05:18.741][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-19 16:05:18.757][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:05:18.758][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:05:18.759][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:05:18.760][FUN] Functions in observer BiodbConfig: [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[2025-04-19 16:05:18.770][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-19 16:05:18.771][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-19 16:05:18.773][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:18.774][ef$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:18.776][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-19 16:05:18.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-19 16:05:18.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:18.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:18.790][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-04-19 16:05:18.791][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-04-19 16:05:18.793][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:18.794][ef$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:18.816][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-04-19 16:05:18.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-04-19 16:05:18.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:18.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:18.821][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-04-19 16:05:18.822][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-04-19 16:05:18.824][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:18.825][ef$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:18.826][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-04-19 16:05:18.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-04-19 16:05:18.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:18.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:18.831][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-19 16:05:18.832][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-19 16:05:18.834][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:18.835][ef$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:18.836][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-19 16:05:18.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-19 16:05:18.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:18.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:18.841][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-19 16:05:18.842][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-19 16:05:18.844][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:18.845][ef$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:18.847][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-19 16:05:18.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-19 16:05:18.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:18.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:18.853][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-04-19 16:05:18.854][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-04-19 16:05:18.855][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:18.856][ef$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:18.858][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-04-19 16:05:18.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-04-19 16:05:18.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:18.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:18.862][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-19 16:05:18.864][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-19 16:05:18.865][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:18.866][ef$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:18.868][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-19 16:05:18.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-19 16:05:18.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:18.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:18.873][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-19 16:05:18.874][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-19 16:05:18.875][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:18.876][ef$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:18.878][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-19 16:05:18.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-19 16:05:18.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:18.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:18.883][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-04-19 16:05:18.884][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-04-19 16:05:18.885][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:18.886][ef$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:18.888][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-04-19 16:05:18.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-04-19 16:05:18.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:18.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:18.893][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-04-19 16:05:18.894][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-04-19 16:05:18.903][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:18.904][ef$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:18.906][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-04-19 16:05:18.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-04-19 16:05:18.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:18.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:18.911][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-19 16:05:18.912][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-19 16:05:18.913][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:18.914][ef$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:18.916][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-19 16:05:18.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-19 16:05:18.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:18.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:18.921][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-19 16:05:18.922][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-19 16:05:18.923][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:18.924][ef$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:18.926][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-19 16:05:18.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-19 16:05:18.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:18.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:18.931][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-19 16:05:18.932][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-19 16:05:18.933][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:18.934][ef$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:18.936][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-19 16:05:18.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-19 16:05:18.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:18.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:18.941][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-19 16:05:18.942][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-19 16:05:18.943][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:18.944][ef$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:18.946][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-19 16:05:18.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-19 16:05:18.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:18.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:18.951][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-19 16:05:18.952][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-19 16:05:18.953][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:18.954][ef$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:18.955][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-19 16:05:18.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-19 16:05:18.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:18.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:18.960][ef$get] Asked field names are: description.
biodb.TRACE[2025-04-19 16:05:18.962][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-04-19 16:05:18.963][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:18.964][ef$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:18.965][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-04-19 16:05:18.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-04-19 16:05:18.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:18.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:18.970][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-19 16:05:18.971][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-19 16:05:18.972][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:18.973][ef$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:18.975][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-19 16:05:18.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-19 16:05:18.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:18.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:18.980][ef$get] Asked field names are: super.class.
biodb.TRACE[2025-04-19 16:05:18.981][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-04-19 16:05:18.982][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:18.983][ef$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:18.985][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2025-04-19 16:05:18.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-04-19 16:05:18.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:18.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:18.990][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-19 16:05:18.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-19 16:05:18.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:18.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:18.995][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-19 16:05:18.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-19 16:05:18.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:18.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:18.999][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-19 16:05:19.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-19 16:05:19.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.031][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-04-19 16:05:19.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-04-19 16:05:19.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.036][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-04-19 16:05:19.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-04-19 16:05:19.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.041][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-04-19 16:05:19.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-04-19 16:05:19.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.045][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-19 16:05:19.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-19 16:05:19.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.050][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-19 16:05:19.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-19 16:05:19.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.055][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-19 16:05:19.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-19 16:05:19.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.064][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-19 16:05:19.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-19 16:05:19.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.069][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-19 16:05:19.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-19 16:05:19.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.074][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-19 16:05:19.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-19 16:05:19.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.078][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-04-19 16:05:19.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-04-19 16:05:19.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.083][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-04-19 16:05:19.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-04-19 16:05:19.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.088][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-04-19 16:05:19.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-04-19 16:05:19.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.093][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-04-19 16:05:19.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-04-19 16:05:19.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.098][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-04-19 16:05:19.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-04-19 16:05:19.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.102][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-04-19 16:05:19.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-04-19 16:05:19.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.107][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-04-19 16:05:19.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-04-19 16:05:19.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.112][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-04-19 16:05:19.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-04-19 16:05:19.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.117][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-04-19 16:05:19.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-04-19 16:05:19.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.122][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-04-19 16:05:19.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-04-19 16:05:19.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.126][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-04-19 16:05:19.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-04-19 16:05:19.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.131][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-04-19 16:05:19.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-04-19 16:05:19.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.136][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-04-19 16:05:19.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-04-19 16:05:19.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.140][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-04-19 16:05:19.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-04-19 16:05:19.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.145][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-04-19 16:05:19.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-04-19 16:05:19.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.150][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-19 16:05:19.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-19 16:05:19.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.155][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-19 16:05:19.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-19 16:05:19.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.160][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-19 16:05:19.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-19 16:05:19.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.164][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-19 16:05:19.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-19 16:05:19.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.169][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-19 16:05:19.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-19 16:05:19.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.174][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-19 16:05:19.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-19 16:05:19.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.179][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-19 16:05:19.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-19 16:05:19.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.184][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-19 16:05:19.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-19 16:05:19.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.188][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-19 16:05:19.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-19 16:05:19.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.193][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-19 16:05:19.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-19 16:05:19.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.198][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-19 16:05:19.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-19 16:05:19.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.203][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-19 16:05:19.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-19 16:05:19.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.207][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-19 16:05:19.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-19 16:05:19.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.212][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-19 16:05:19.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-19 16:05:19.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.217][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-19 16:05:19.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-19 16:05:19.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.222][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-19 16:05:19.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-19 16:05:19.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.226][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-19 16:05:19.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-19 16:05:19.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.231][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-19 16:05:19.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-19 16:05:19.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.236][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-19 16:05:19.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-19 16:05:19.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.245][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-19 16:05:19.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-19 16:05:19.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.250][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-19 16:05:19.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-19 16:05:19.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.254][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-04-19 16:05:19.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-04-19 16:05:19.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.259][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-04-19 16:05:19.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-04-19 16:05:19.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.264][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-04-19 16:05:19.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-04-19 16:05:19.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.269][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-19 16:05:19.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-19 16:05:19.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.274][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-19 16:05:19.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-19 16:05:19.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.278][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-19 16:05:19.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-19 16:05:19.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.283][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-04-19 16:05:19.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-19 16:05:19.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.288][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-19 16:05:19.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-19 16:05:19.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.293][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-19 16:05:19.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-19 16:05:19.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.297][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-19 16:05:19.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-19 16:05:19.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.302][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-04-19 16:05:19.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-19 16:05:19.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.322][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-19 16:05:19.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-19 16:05:19.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.327][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-19 16:05:19.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-19 16:05:19.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.331][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-19 16:05:19.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-19 16:05:19.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.336][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-19 16:05:19.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-19 16:05:19.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.341][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-19 16:05:19.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-19 16:05:19.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.346][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-04-19 16:05:19.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-04-19 16:05:19.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.351][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-04-19 16:05:19.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-04-19 16:05:19.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.355][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-19 16:05:19.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-19 16:05:19.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.360][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-04-19 16:05:19.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-04-19 16:05:19.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.365][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-19 16:05:19.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-19 16:05:19.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.370][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-19 16:05:19.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-19 16:05:19.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.374][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-19 16:05:19.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-19 16:05:19.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.379][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-19 16:05:19.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-19 16:05:19.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.384][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-19 16:05:19.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-19 16:05:19.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.389][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-19 16:05:19.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-19 16:05:19.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-04-19 16:05:19.394][biodb$getFactory()$createEntryFromCo ...] Accession numbers: HMDB0000001.
biodb.TRACE[2025-04-19 16:05:19.397][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-19 16:05:19.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-19 16:05:19.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.402][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-04-19 16:05:19.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-04-19 16:05:19.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.411][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-04-19 16:05:19.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-04-19 16:05:19.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.416][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-04-19 16:05:19.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-04-19 16:05:19.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.455][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-19 16:05:19.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-19 16:05:19.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.473][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-04-19 16:05:19.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-04-19 16:05:19.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.484][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-19 16:05:19.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-19 16:05:19.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.489][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-19 16:05:19.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-19 16:05:19.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.493][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-19 16:05:19.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-19 16:05:19.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.500][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-19 16:05:19.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-19 16:05:19.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.505][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-19 16:05:19.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-19 16:05:19.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.509][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-19 16:05:19.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-19 16:05:19.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.514][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-04-19 16:05:19.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-04-19 16:05:19.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.519][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-04-19 16:05:19.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-04-19 16:05:19.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.524][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-04-19 16:05:19.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-04-19 16:05:19.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.538][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-19 16:05:19.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-19 16:05:19.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.543][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-19 16:05:19.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-19 16:05:19.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.548][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-19 16:05:19.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-19 16:05:19.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.552][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-19 16:05:19.554][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-19 16:05:19.555][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.556][ef$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.557][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-04-19 16:05:19.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-19 16:05:19.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.572][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-04-19 16:05:19.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-04-19 16:05:19.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.577][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-04-19 16:05:19.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-04-19 16:05:19.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.582][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-04-19 16:05:19.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-04-19 16:05:19.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.586][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-04-19 16:05:19.588][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-04-19 16:05:19.589][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.590][ef$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.591][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-04-19 16:05:19.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-04-19 16:05:19.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.606][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-04-19 16:05:19.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-04-19 16:05:19.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.616][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-04-19 16:05:19.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-04-19 16:05:19.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.621][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-04-19 16:05:19.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-04-19 16:05:19.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.625][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-04-19 16:05:19.627][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-04-19 16:05:19.628][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.629][ef$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.630][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-04-19 16:05:19.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-04-19 16:05:19.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.644][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-19 16:05:19.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-19 16:05:19.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.649][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-19 16:05:19.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-19 16:05:19.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.654][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-19 16:05:19.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-19 16:05:19.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.659][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-19 16:05:19.660][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-19 16:05:19.661][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.662][ef$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.663][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-19 16:05:19.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-19 16:05:19.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.678][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-19 16:05:19.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-19 16:05:19.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.683][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-19 16:05:19.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-19 16:05:19.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.687][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-19 16:05:19.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-19 16:05:19.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.692][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-19 16:05:19.693][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-19 16:05:19.694][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.696][ef$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.697][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-19 16:05:19.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-19 16:05:19.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.711][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-19 16:05:19.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-19 16:05:19.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.716][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-19 16:05:19.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-19 16:05:19.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.721][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-19 16:05:19.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-19 16:05:19.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.725][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-19 16:05:19.727][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-19 16:05:19.728][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.729][ef$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.730][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-19 16:05:19.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-19 16:05:19.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.744][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-19 16:05:19.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-19 16:05:19.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.749][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-19 16:05:19.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-19 16:05:19.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.754][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-19 16:05:19.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-19 16:05:19.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.759][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-19 16:05:19.760][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-19 16:05:19.761][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.762][ef$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.763][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-04-19 16:05:19.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-04-19 16:05:19.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.778][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-04-19 16:05:19.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-04-19 16:05:19.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.783][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-04-19 16:05:19.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-04-19 16:05:19.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.788][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-04-19 16:05:19.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-04-19 16:05:19.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.797][ef$get] Asked field names are: description.
biodb.TRACE[2025-04-19 16:05:19.798][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-04-19 16:05:19.799][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.800][ef$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.802][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-04-19 16:05:19.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-04-19 16:05:19.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.816][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-19 16:05:19.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-19 16:05:19.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.821][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-19 16:05:19.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-19 16:05:19.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.826][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-19 16:05:19.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-19 16:05:19.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.830][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-19 16:05:19.832][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-19 16:05:19.833][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.834][ef$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.835][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-04-19 16:05:19.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-19 16:05:19.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.850][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-04-19 16:05:19.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-04-19 16:05:19.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.855][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-04-19 16:05:19.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-04-19 16:05:19.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.859][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-04-19 16:05:19.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-04-19 16:05:19.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.864][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-04-19 16:05:19.865][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-04-19 16:05:19.866][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.868][ef$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.869][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-04-19 16:05:19.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-04-19 16:05:19.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.883][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-19 16:05:19.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-19 16:05:19.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.888][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-19 16:05:19.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-19 16:05:19.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.892][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-19 16:05:19.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-19 16:05:19.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.897][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-19 16:05:19.899][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-19 16:05:19.900][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.901][ef$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.902][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-19 16:05:19.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-19 16:05:19.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.916][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-04-19 16:05:19.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-04-19 16:05:19.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.921][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-04-19 16:05:19.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-04-19 16:05:19.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.926][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-04-19 16:05:19.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-04-19 16:05:19.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.930][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-04-19 16:05:19.932][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-04-19 16:05:19.933][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.934][ef$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.935][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-04-19 16:05:19.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-04-19 16:05:19.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.949][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-04-19 16:05:19.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-04-19 16:05:19.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.954][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-04-19 16:05:19.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-04-19 16:05:19.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.959][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-04-19 16:05:19.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-04-19 16:05:19.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.964][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-04-19 16:05:19.965][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-04-19 16:05:19.966][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.967][ef$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.968][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-04-19 16:05:19.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-04-19 16:05:19.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.987][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-04-19 16:05:19.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-04-19 16:05:19.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.992][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-04-19 16:05:19.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-04-19 16:05:19.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:19.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:19.997][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-04-19 16:05:19.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-04-19 16:05:20.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:20.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:20.002][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-04-19 16:05:20.003][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-04-19 16:05:20.005][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:20.006][ef$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:20.007][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-04-19 16:05:20.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-04-19 16:05:20.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:20.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:20.021][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-19 16:05:20.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-19 16:05:20.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:20.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:20.026][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-19 16:05:20.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-19 16:05:20.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:20.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:20.031][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-19 16:05:20.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-19 16:05:20.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:20.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:20.036][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-19 16:05:20.037][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-19 16:05:20.038][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:20.039][ef$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:20.040][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-04-19 16:05:20.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-19 16:05:20.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:20.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:20.055][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-19 16:05:20.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-19 16:05:20.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:20.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:20.060][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-19 16:05:20.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-19 16:05:20.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:20.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:20.064][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-19 16:05:20.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-19 16:05:20.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:20.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:20.069][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-19 16:05:20.070][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-19 16:05:20.071][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:20.073][ef$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:20.074][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-04-19 16:05:20.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-19 16:05:20.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:20.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:20.088][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-19 16:05:20.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-19 16:05:20.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:20.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:20.093][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-19 16:05:20.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-19 16:05:20.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:20.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:20.098][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-19 16:05:20.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-19 16:05:20.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:20.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:20.103][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-19 16:05:20.104][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-19 16:05:20.105][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:20.106][ef$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:20.107][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-19 16:05:20.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-19 16:05:20.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:20.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:20.121][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-19 16:05:20.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-19 16:05:20.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:20.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:20.126][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-19 16:05:20.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-19 16:05:20.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:20.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:20.131][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-19 16:05:20.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-19 16:05:20.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:20.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:20.136][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-19 16:05:20.137][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-19 16:05:20.138][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:20.139][ef$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:20.140][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-19 16:05:20.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-19 16:05:20.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:20.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:20.159][ef$get] Asked field names are: accession.
biodb.TRACE[2025-04-19 16:05:20.161][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-04-19 16:05:20.162][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:20.163][ef$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:20.170][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-04-19 16:05:20.171][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-04-19 16:05:20.172][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:20.173][ef$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:20.180][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-04-19 16:05:20.181][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-04-19 16:05:20.182][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:20.183][ef$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:20.190][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-04-19 16:05:20.191][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-04-19 16:05:20.192][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:20.194][ef$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:20.200][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-04-19 16:05:20.201][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-04-19 16:05:20.203][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:20.204][ef$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:20.210][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-04-19 16:05:20.212][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-04-19 16:05:20.213][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:20.214][ef$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:20.220][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-04-19 16:05:20.222][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-04-19 16:05:20.223][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:20.224][ef$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:20.230][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-04-19 16:05:20.232][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-04-19 16:05:20.233][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:20.234][ef$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:20.241][ef$get] Asked field names are: description.
biodb.TRACE[2025-04-19 16:05:20.242][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-04-19 16:05:20.243][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:20.244][ef$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:20.251][ef$get] Asked field names are: formula.
biodb.TRACE[2025-04-19 16:05:20.252][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-04-19 16:05:20.253][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:20.254][ef$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:20.261][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-04-19 16:05:20.262][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-04-19 16:05:20.263][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:20.264][ef$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:20.271][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-04-19 16:05:20.272][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-04-19 16:05:20.274][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:20.275][ef$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:20.281][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-04-19 16:05:20.282][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-04-19 16:05:20.284][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:20.285][ef$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:20.291][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-04-19 16:05:20.292][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-04-19 16:05:20.294][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:20.295][ef$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:20.301][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-19 16:05:20.303][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-19 16:05:20.304][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:20.305][ef$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:20.311][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-19 16:05:20.312][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-04-19 16:05:20.314][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:20.315][ef$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:20.321][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-04-19 16:05:20.322][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-04-19 16:05:20.324][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:20.325][ef$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:20.331][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-04-19 16:05:20.332][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-04-19 16:05:20.334][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:20.335][ef$get] fields variable is a list.
biodb.INFO [2025-04-19 16:05:20.346][biodb::testThat]
biodb.INFO [2025-04-19 16:05:20.348][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-04-19 16:05:20.349][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-19 16:05:20.350][biodb::testThat]
biodb.DEBUG[2025-04-19 16:05:20.368][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-04-19 16:05:20.374][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.INFO [2025-04-19 16:05:20.380][self$getFolderPath] Create cache folder "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34" for "hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34".
biodb.DEBUG[2025-04-19 16:05:20.383][self$isDownloaded] Database hmdb.metabolites has not yet been downloaded.
biodb.INFO [2025-04-19 16:05:20.384][self$download] Downloading whole database of hmdb.metabolites.
biodb.INFO [2025-04-19 16:05:20.385][private$doDownload] Downloading HMDB metabolite database at "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip" ...
biodb.DEBUG[2025-04-19 16:05:20.388][sched$downloadFile] Downloading file "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
trying URL 'http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip'
Content type 'application/zip' length 953913010 bytes (909.7 MB)

downloaded 13.5 MB

biodb.INFO [2025-04-19 16:05:21.645][biodb::testThat]
biodb.INFO [2025-04-19 16:05:21.647][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-04-19 16:05:21.648][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-19 16:05:21.649][biodb::testThat]
biodb.TRACE[2025-04-19 16:05:21.653][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-19 16:05:21.654][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-19 16:05:21.655][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:21.656][ef$get] fields variable is a list.
biodb.DEBUG[2025-04-19 16:05:21.658][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "name".
biodb.DEBUG[2025-04-19 16:05:21.681][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-04-19 16:05:21.726][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-04-19 16:05:21.729][self$isDownloaded] Database hmdb.metabolites has not yet been downloaded.
biodb.INFO [2025-04-19 16:05:21.730][self$download] Downloading whole database of hmdb.metabolites.
biodb.INFO [2025-04-19 16:05:21.731][private$doDownload] Downloading HMDB metabolite database at "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip" ...
biodb.DEBUG[2025-04-19 16:05:21.745][sched$downloadFile] Downloading file "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
trying URL 'http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip'
Content type 'application/zip' length 953913010 bytes (909.7 MB)

downloaded 0 bytes

biodb.INFO [2025-04-19 16:05:21.959][biodb::testThat]
biodb.INFO [2025-04-19 16:05:21.961][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-04-19 16:05:21.962][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-19 16:05:21.963][biodb::testThat]
biodb.DEBUG[2025-04-19 16:05:21.973][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-04-19 16:05:21.974][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-04-19 16:05:21.976][self$isDownloaded] Database hmdb.metabolites has not yet been downloaded.
biodb.INFO [2025-04-19 16:05:21.978][self$download] Downloading whole database of hmdb.metabolites.
biodb.INFO [2025-04-19 16:05:21.979][private$doDownload] Downloading HMDB metabolite database at "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip" ...
biodb.DEBUG[2025-04-19 16:05:21.981][sched$downloadFile] Downloading file "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.TRACE[2025-04-19 16:05:22.000][cch$addFilesToCache] Moving files to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/tmp\hmdb.metabolites759c1c9ffaezip".
biodb.TRACE[2025-04-19 16:05:22.002][private$doAddFilesToCache] Destination files are [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip".
biodb.DEBUG[2025-04-19 16:05:22.016][cch$addFilesToCache] Done adding files.
biodb.DEBUG[2025-04-19 16:05:22.018][self$getDownloadPath] Download path of hmdb.metabolites is "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip".
biodb.DEBUG[2025-04-19 16:05:22.020][self$getDownloadPath] Download path of hmdb.metabolites is "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip".
biodb.ERROR[2025-04-19 16:05:22.021][self$download] File C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip does not exists. Downloading went wrong.
biodb.INFO [2025-04-19 16:05:22.036][biodb::testThat]
biodb.INFO [2025-04-19 16:05:22.037][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-04-19 16:05:22.039][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-19 16:05:22.040][biodb::testThat]
biodb.DEBUG[2025-04-19 16:05:22.045][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-04-19 16:05:22.046][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-04-19 16:05:22.048][self$isDownloaded] Database hmdb.metabolites has not yet been downloaded.
biodb.INFO [2025-04-19 16:05:22.049][self$download] Downloading whole database of hmdb.metabolites.
biodb.INFO [2025-04-19 16:05:22.050][private$doDownload] Downloading HMDB metabolite database at "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip" ...
biodb.DEBUG[2025-04-19 16:05:22.053][sched$downloadFile] Downloading file "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.TRACE[2025-04-19 16:05:22.073][cch$addFilesToCache] Moving files to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/tmp\hmdb.metabolites759c653a3f18zip".
biodb.TRACE[2025-04-19 16:05:22.074][private$doAddFilesToCache] Destination files are [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip".
biodb.DEBUG[2025-04-19 16:05:22.084][cch$addFilesToCache] Done adding files.
biodb.DEBUG[2025-04-19 16:05:22.086][self$getDownloadPath] Download path of hmdb.metabolites is "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip".
biodb.DEBUG[2025-04-19 16:05:22.088][self$getDownloadPath] Download path of hmdb.metabolites is "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip".
biodb.ERROR[2025-04-19 16:05:22.089][self$download] File C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip does not exists. Downloading went wrong.
biodb.INFO [2025-04-19 16:05:22.104][biodb::testThat]
biodb.INFO [2025-04-19 16:05:22.105][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-04-19 16:05:22.106][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-19 16:05:22.108][biodb::testThat]
biodb.INFO [2025-04-19 16:05:22.119][biodb::testThat]
biodb.INFO [2025-04-19 16:05:22.120][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-04-19 16:05:22.121][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-19 16:05:22.122][biodb::testThat]
biodb.INFO [2025-04-19 16:05:22.134][biodb::testThat]
biodb.INFO [2025-04-19 16:05:22.135][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-04-19 16:05:22.136][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-19 16:05:22.137][biodb::testThat]
biodb.DEBUG[2025-04-19 16:05:22.141][function(conn, opt)] Trying to download "http://www.hmdb.ca/metabolites/HMDB0000001".
biodb.DEBUG[2025-04-19 16:05:23.770][getUrlContent] Use RCurl for downloading content of URL http://www.hmdb.ca/metabolites/HMDB0000001.
biodb.INFO [2025-04-19 16:05:23.846][biodb::testThat]
biodb.INFO [2025-04-19 16:05:23.847][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-04-19 16:05:23.848][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-04-19 16:05:23.850][biodb::testThat]
biodb.DEBUG[2025-04-19 16:05:24.044][getUrlContent] Use RCurl for downloading content of URL http://www.hmdb.ca/structures/HMDB0000001/image.png.
biodb.TRACE[2025-04-19 16:05:24.126][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-19 16:05:24.127][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-19 16:05:24.128][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:24.130][ef$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:24.131][ef$get] Asked field names are: description.
biodb.TRACE[2025-04-19 16:05:24.132][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-04-19 16:05:24.133][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:24.134][ef$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:24.136][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-04-19 16:05:24.137][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-04-19 16:05:24.138][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:24.139][ef$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:24.141][ef$get] Asked field names are: name.
biodb.TRACE[2025-04-19 16:05:24.142][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-04-19 16:05:24.143][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:24.144][ef$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:24.145][ef$get] Asked field names are: description.
biodb.TRACE[2025-04-19 16:05:24.146][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-04-19 16:05:24.148][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:24.149][ef$get] fields variable is a list.
biodb.TRACE[2025-04-19 16:05:24.150][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-04-19 16:05:24.151][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-04-19 16:05:24.152][ef$get] 1 fields were returned.
biodb.TRACE[2025-04-19 16:05:24.153][ef$get] fields variable is a list.
biodb.INFO [2025-04-19 16:05:24.155][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-04-19 16:05:24.156][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler
biodb.INFO [2025-04-19 16:05:24.157][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2025-04-19 16:05:24.158][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-04-19 16:05:24.159][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-04-19 16:05:24.160][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-04-19 16:05:24.161][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-04-19 16:05:24.163][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-04-19 16:05:24.164][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-04-19 16:05:24.165][FUN] Functions in observer 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 4 | WARN 10 | SKIP 0 | PASS 113 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_long_100_generic.R:42:1'): RT unit is defined when there is an RT value. ──
Error in `utils::download.file(url = url, destfile = dest.file, mode = "wb", 
    method = "auto", cacheOK = FALSE, quiet = FALSE)`: download from 'http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip' failed
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
 3.   └─conn$getBiodb()$getFactory()$getEntry(...)
 4.     └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
 5.       └─conn$getEntryContent(ids)
 6.         └─self$download()
 7.           └─private$doDownload()
 8.             └─sched$downloadFile(url = zip.url, dest.file = tmpFile)
 9.               └─utils::download.file(...)
── Error ('test_long_100_generic.R:42:1'): We can search for an entry by searchable field ──
Error in `utils::download.file(url = url, destfile = dest.file, mode = "wb", 
    method = "auto", cacheOK = FALSE, quiet = FALSE)`: download from 'http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip' failed
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
  3.   └─conn$getEntry(id, drop = TRUE)
  4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
  5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  6.         └─conn$getEntryContent(ids)
  7.           └─self$download()
  8.             └─private$doDownload()
  9.               └─sched$downloadFile(url = zip.url, dest.file = tmpFile)
 10.                 └─utils::download.file(...)
── Error ('test_long_100_generic.R:42:1'): We can search for an entry by name. ──
Error in `error("File %s does not exists. Downloading went wrong.", self$getDownloadPath())`: File C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip does not exists. Downloading went wrong.
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
 3.   └─conn$getEntry(id, drop = TRUE)
 4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
 5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
 6.         └─conn$getEntryContent(ids)
 7.           └─self$download()
 8.             └─biodb::error(...)
── Error ('test_long_100_generic.R:42:1'): We can load an entry from the database. ──
Error in `error("File %s does not exists. Downloading went wrong.", self$getDownloadPath())`: File C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip does not exists. Downloading went wrong.
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
 3.   └─opt$refEntries$getRealEntry(id)
 4.     └─self$getRealEntries(ids = id)
 5.       └─private$bdb$getFactory()$getEntry(...)
 6.         └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
 7.           └─conn$getEntryContent(ids)
 8.             └─self$download()
 9.               └─biodb::error(...)

[ FAIL 4 | WARN 10 | SKIP 0 | PASS 113 ]
Error: Test failures
Execution halted

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbHmdb_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbuild/bbs-3.21-bioc-longtests/meat/biodbHmdb.Rcheck'
* using R version 4.5.0 RC (2025-04-04 r88126 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using options '--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error'
* checking for file 'biodbHmdb/DESCRIPTION' ... OK
* this is package 'biodbHmdb' version '1.14.0'
* 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 whether package 'biodbHmdb' can be installed ... WARNING
Found the following significant warnings:
  EntryMaker.hpp:23:21: warning: 'EntryMaker::accession_tag' will be initialized after [-Wreorder]
  EntryMaker.hpp:22:14: warning:   'bool EntryMaker::closed' [-Wreorder]
  EntryMaker.cpp:5:1: warning:   when initialized here [-Wreorder]
See 'E:/biocbuild/bbs-3.21-bioc-longtests/meat/biodbHmdb.Rcheck/00install.out' for details.
* used C++ compiler: 'G__~1.EXE (GCC) 14.2.0'
* 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 dependencies in R code ... NOTE
Namespace in Imports field not imported from: 'zip'
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  'HmdbMetabolitesConn' 'HmdbMetabolitesEntry' 'hmdbToSqlite'
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking files in 'vignettes' ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in 'longtests' ... OK
* checking tests in 'longtests' ...
  Running 'testthat.R'
 ERROR
Running the tests in 'longtests/testthat.R' failed.
Last 13 lines of output:
  Backtrace:
      ▆
   1. ├─base::do.call(fct, params)
   2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
   3.   └─opt$refEntries$getRealEntry(id)
   4.     └─self$getRealEntries(ids = id)
   5.       └─private$bdb$getFactory()$getEntry(...)
   6.         └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
   7.           └─conn$getEntryContent(ids)
   8.             └─self$download()
   9.               └─biodb::error(...)
  
  [ FAIL 4 | WARN 10 | SKIP 0 | PASS 113 ]
  Error: Test failures
  Execution halted
* DONE

Status: 1 ERROR, 2 WARNINGs, 1 NOTE
See
  'E:/biocbuild/bbs-3.21-bioc-longtests/meat/biodbHmdb.Rcheck/00check.log'
for details.

Installation output

biodbHmdb.Rcheck/00install.out

* installing *source* package 'biodbHmdb' ...
** this is package 'biodbHmdb' version '1.14.0'
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 14.2.0'
g++ -std=gnu++17  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/testthat/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c EntryMaker.cpp -o EntryMaker.o
In file included from EntryMaker.cpp:1:
EntryMaker.hpp: In constructor 'EntryMaker::EntryMaker()':
EntryMaker.hpp:23:21: warning: 'EntryMaker::accession_tag' will be initialized after [-Wreorder]
   23 |         TagDetector accession_tag;
      |                     ^~~~~~~~~~~~~
EntryMaker.hpp:22:14: warning:   'bool EntryMaker::closed' [-Wreorder]
   22 |         bool closed;
      |              ^~~~~~
EntryMaker.cpp:5:1: warning:   when initialized here [-Wreorder]
    5 | EntryMaker::EntryMaker() :
      | ^~~~~~~~~~
g++ -std=gnu++17  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/testthat/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c FileEntryMaker.cpp -o FileEntryMaker.o
g++ -std=gnu++17  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/testthat/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/testthat/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c StringEnrtryMaker.cpp -o StringEnrtryMaker.o
g++ -std=gnu++17  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/testthat/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c TagDetector.cpp -o TagDetector.o
g++ -std=gnu++17  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/testthat/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c XmlSplitter.cpp -o XmlSplitter.o
g++ -std=gnu++17  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/testthat/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c extractXmlEntries.cpp -o extractXmlEntries.o
g++ -std=gnu++17  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/testthat/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c test-100-TagDetector.cpp -o test-100-TagDetector.o
g++ -std=gnu++17  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/testthat/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c test-150-StringEntryMaker.cpp -o test-150-StringEntryMaker.o
g++ -std=gnu++17  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/testthat/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c test-200-XmlSplitter.cpp -o test-200-XmlSplitter.o
g++ -std=gnu++17  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/testthat/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c test-runner.cpp -o test-runner.o
g++ -std=gnu++17 -shared -s -static-libgcc -o biodbHmdb.dll tmp.def EntryMaker.o FileEntryMaker.o RcppExports.o StringEnrtryMaker.o TagDetector.o XmlSplitter.o extractXmlEntries.o test-100-TagDetector.o test-150-StringEntryMaker.o test-200-XmlSplitter.o test-runner.o -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib -LE:/biocbuild/bbs-3.21-bioc/R/bin/x64 -lR
installing to E:/biocbuild/bbs-3.21-bioc-longtests/meat/biodbHmdb.Rcheck/00LOCK-biodbHmdb/00new/biodbHmdb/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
** help
No man pages found in package  'biodbHmdb' 
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (biodbHmdb)