Back to Long Tests report for BioC 3.21

This page was generated on 2025-02-08 23:55 -0500 (Sat, 08 Feb 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" 4719
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" 4480
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences" 4491
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 1.13.0  (landing page)
Pierrick Roger
Snapshot Date: 2025-02-08 11:09 -0500 (Sat, 08 Feb 2025)
git_url: https://git.bioconductor.org/packages/biodbHmdb
git_branch: devel
git_last_commit: d2b9830
git_last_commit_date: 2024-10-29 11:06:39 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  WARNINGS  
palomino7Windows Server 2022 Datacenter / x64  ERROR  
lconwaymacOS 12.7.1 Monterey / x86_64  ERROR  

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: 1.13.0
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_1.13.0.tar.gz
StartedAt: 2025-02-08 16:03:05 -0500 (Sat, 08 Feb 2025)
EndedAt: 2025-02-08 16:09:28 -0500 (Sat, 08 Feb 2025)
EllapsedTime: 383.4 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbHmdb.Rcheck
Warnings: NA

Tests output

biodbHmdb.Rcheck/tests/testthat.Rout.fail


R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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> # 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 [2025-02-08 16:04:37.503][biodb::testContext]
biodb.INFO [2025-02-08 16:04:37.506][biodb::testContext] ********************************************************************************
biodb.INFO [2025-02-08 16:04:37.507][biodb::testContext] Test context - Generic long tests
biodb.INFO [2025-02-08 16:04:37.508][biodb::testContext] ********************************************************************************
biodb.INFO [2025-02-08 16:04:37.509][biodb::testContext]
biodb.INFO [2025-02-08 16:04:37.516][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2025-02-08 16:04:37.518][self$loadDefinitions] Load definitions from file "E:/biocbuild/bbs-3.21-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2025-02-08 16:04:37.526][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-02-08 16:04:37.527][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-02-08 16:04:37.528][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-02-08 16:04:37.529][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:04:37.530][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:04:37.531][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:04:37.533][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-02-08 16:04:37.548][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-02-08 16:04:37.549][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:04:37.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:04:37.551][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:04:37.552][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-02-08 16:04:37.554][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-02-08 16:04:37.555][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:04:37.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:04:37.557][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:04:37.558][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-02-08 16:04:37.559][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-02-08 16:04:37.560][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-02-08 16:04:37.561][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:04:37.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:04:37.563][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[2025-02-08 16:04:37.565][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-02-08 16:04:37.566][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-02-08 16:04:37.567][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-02-08 16:04:37.568][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:04:37.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:04:37.570][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:04:37.571][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-02-08 16:04:37.572][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-02-08 16:04:37.573][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:04:37.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:04:37.575][FUN] Functions in observer BiodbConfig: [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[2025-02-08 16:04:37.577][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-02-08 16:04:37.578][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-02-08 16:04:37.579][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-02-08 16:04:37.580][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:04:37.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:04:37.582][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:04:37.583][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-02-08 16:04:37.584][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-02-08 16:04:37.585][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:04:37.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:04:37.587][FUN] Functions in observer BiodbConfig: [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[2025-02-08 16:04:37.589][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-02-08 16:04:37.590][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-02-08 16:04:37.591][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-02-08 16:04:37.592][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:04:37.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:04:37.594][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:04:37.595][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-02-08 16:04:37.596][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-02-08 16:04:37.597][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-02-08 16:04:37.599][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-02-08 16:04:37.600][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-02-08 16:04:37.601][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-02-08 16:04:37.602][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:04:37.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:04:37.604][FUN] Functions in observer BiodbConfig: [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[2025-02-08 16:04:37.605][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-02-08 16:04:37.606][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-02-08 16:04:37.607][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:04:37.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:04:37.610][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:04:37.611][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-02-08 16:04:37.612][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-02-08 16:04:37.613][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:04:37.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:04:37.615][FUN] Functions in observer BiodbConfig: [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[2025-02-08 16:04:37.616][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-02-08 16:04:37.617][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-02-08 16:04:37.618][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:04:37.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:04:37.620][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:04:37.622][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-02-08 16:04:37.623][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-02-08 16:04:37.624][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:04:37.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:04:37.626][FUN] Functions in observer BiodbConfig: [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[2025-02-08 16:04:37.627][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-02-08 16:04:37.628][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-02-08 16:04:37.629][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:04:37.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:04:37.631][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:04:37.632][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-02-08 16:04:37.634][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-02-08 16:04:37.637][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-02-08 16:04:37.638][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:04:37.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:04:37.640][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:04:37.641][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-02-08 16:04:37.642][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-02-08 16:04:37.644][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-02-08 16:04:37.645][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:04:37.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:04:37.647][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:04:37.650][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-02-08 16:04:37.677][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-02-08 16:04:37.698][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-02-08 16:04:37.699][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-08 16:04:37.700][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-08 16:04:37.701][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-08 16:04:37.702][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-08 16:04:37.704][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-08 16:04:37.705][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-08 16:04:37.706][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-02-08 16:04:37.707][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-08 16:04:37.708][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-02-08 16:04:37.710][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-02-08 16:04:37.711][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-08 16:04:37.712][self$setPropertyValue]
biodb.DEBUG[2025-02-08 16:04:37.713][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-08 16:04:37.714][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-02-08 16:04:37.714][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-02-08 16:04:37.714][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-02-08 16:04:37.714][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-02-08 16:04:37.714][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-02-08 16:04:37.716][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-08 16:04:37.717][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-08 16:04:37.718][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-08 16:04:37.719][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-08 16:04:37.720][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-08 16:04:37.721][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-08 16:04:37.722][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-08 16:04:37.723][self$setPropertyValue]
biodb.DEBUG[2025-02-08 16:04:37.725][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-08 16:04:37.726][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-08 16:04:37.727][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-08 16:04:37.728][self$setPropertyValue]
biodb.DEBUG[2025-02-08 16:04:37.729][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-02-08 16:04:37.731][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-02-08 16:04:37.733][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-02-08 16:04:37.734][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-08 16:04:37.735][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-08 16:04:37.736][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-08 16:04:37.737][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-08 16:04:37.738][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-08 16:04:37.740][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-08 16:04:37.741][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-02-08 16:04:37.742][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-08 16:04:37.743][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-02-08 16:04:37.744][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-02-08 16:04:37.746][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-08 16:04:37.747][self$setPropertyValue]
biodb.DEBUG[2025-02-08 16:04:37.748][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-08 16:04:37.749][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-02-08 16:04:37.749][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-02-08 16:04:37.749][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-02-08 16:04:37.749][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-02-08 16:04:37.749][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-02-08 16:04:37.750][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-08 16:04:37.751][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-08 16:04:37.752][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-08 16:04:37.754][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-08 16:04:37.755][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-08 16:04:37.756][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-08 16:04:37.757][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-08 16:04:37.758][self$setPropertyValue]
biodb.DEBUG[2025-02-08 16:04:37.759][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-08 16:04:37.760][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-08 16:04:37.761][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-08 16:04:37.763][self$setPropertyValue]
biodb.DEBUG[2025-02-08 16:04:37.764][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-02-08 16:04:37.766][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-02-08 16:04:37.767][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-02-08 16:04:37.768][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-08 16:04:37.769][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-08 16:04:37.771][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-08 16:04:37.772][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-08 16:04:37.773][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-08 16:04:37.774][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-08 16:04:37.775][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-02-08 16:04:37.776][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-08 16:04:37.778][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-02-08 16:04:37.779][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-02-08 16:04:37.780][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-08 16:04:37.781][self$setPropertyValue]
biodb.DEBUG[2025-02-08 16:04:37.782][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-08 16:04:37.783][self$setPropertyValue]
biodb.DEBUG[2025-02-08 16:04:37.785][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-08 16:04:37.786][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-08 16:04:37.787][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-08 16:04:37.788][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-08 16:04:37.789][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-08 16:04:37.790][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-08 16:04:37.791][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-08 16:04:37.792][self$setPropertyValue]
biodb.DEBUG[2025-02-08 16:04:37.793][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-08 16:04:37.795][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-08 16:04:37.796][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-08 16:04:37.797][self$setPropertyValue]
biodb.DEBUG[2025-02-08 16:04:37.798][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-02-08 16:04:37.800][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-02-08 16:04:37.801][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-02-08 16:04:37.802][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-08 16:04:37.804][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-08 16:04:37.805][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-08 16:04:37.806][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-08 16:04:37.807][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-08 16:04:37.808][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-08 16:04:37.809][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-02-08 16:04:37.811][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-08 16:04:37.812][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-02-08 16:04:37.813][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-02-08 16:04:37.814][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-08 16:04:37.815][self$setPropertyValue]
biodb.DEBUG[2025-02-08 16:04:37.816][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-08 16:04:37.818][self$setPropertyValue]
biodb.DEBUG[2025-02-08 16:04:37.819][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-08 16:04:37.820][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-08 16:04:37.821][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-08 16:04:37.822][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-08 16:04:37.823][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-08 16:04:37.824][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-08 16:04:37.826][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-08 16:04:37.827][self$setPropertyValue]
biodb.DEBUG[2025-02-08 16:04:37.828][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-08 16:04:37.829][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-08 16:04:37.830][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-08 16:04:37.831][self$setPropertyValue]
biodb.DEBUG[2025-02-08 16:04:37.835][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-02-08 16:04:37.836][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:04:37.837][FUN] Functions in observer BiodbConfig: [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[2025-02-08 16:04:37.838][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:04:37.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:04:37.840][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:04:37.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:04:37.842][FUN] Functions in observer BiodbConfig: [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[2025-02-08 16:04:37.843][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:04:37.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:04:37.845][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:04:37.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:04:37.847][FUN] Functions in observer BiodbConfig: [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[2025-02-08 16:04:37.848][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:04:37.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:04:37.850][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:04:37.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:04:37.853][FUN] Functions in observer BiodbConfig: [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[2025-02-08 16:04:37.854][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:04:37.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:04:37.856][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:04:37.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:04:37.858][FUN] Functions in observer BiodbConfig: [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[2025-02-08 16:04:37.859][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:04:37.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:04:37.861][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:04:37.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:04:37.863][FUN] Functions in observer BiodbConfig: [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[2025-02-08 16:04:37.864][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:04:37.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:04:37.866][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:04:37.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:04:37.869][FUN] Functions in observer BiodbConfig: [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[2025-02-08 16:04:37.870][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:04:37.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:04:37.872][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:04:37.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:04:37.874][FUN] Functions in observer BiodbConfig: [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[2025-02-08 16:04:37.875][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:04:37.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:04:37.877][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:04:37.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:04:37.879][FUN] Functions in observer BiodbConfig: [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[2025-02-08 16:04:37.880][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:04:37.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:04:37.882][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:04:37.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:04:37.885][FUN] Functions in observer BiodbConfig: [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[2025-02-08 16:04:37.886][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:04:37.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:04:37.888][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:04:37.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:04:37.890][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:04:37.891][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:04:37.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:04:37.893][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:04:37.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:04:37.895][FUN] Functions in observer BiodbConfig: [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[2025-02-08 16:04:37.896][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:04:37.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:04:37.898][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:04:37.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:04:37.900][FUN] Functions in observer BiodbConfig: [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[2025-02-08 16:04:37.902][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:04:37.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:04:37.904][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:04:37.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:04:37.906][FUN] Functions in observer BiodbConfig: [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[2025-02-08 16:04:37.907][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:04:37.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:04:37.914][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:04:37.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:04:37.916][FUN] Functions in observer BiodbConfig: [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[2025-02-08 16:04:37.917][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:04:37.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:04:37.919][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:04:37.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:04:37.921][FUN] Functions in observer BiodbConfig: [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[2025-02-08 16:04:37.922][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:04:37.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:04:37.924][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:04:37.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:04:37.927][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[2025-02-08 16:04:37.928][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:04:37.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:04:37.930][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:04:37.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:04:37.932][FUN] Functions in observer BiodbConfig: [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[2025-02-08 16:04:37.933][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-02-08 16:04:37.937][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-02-08 16:04:37.939][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-02-08 16:04:37.940][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-02-08 16:04:37.942][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-02-08 16:04:37.943][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-02-08 16:04:37.945][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-02-08 16:04:37.947][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-02-08 16:04:37.948][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-02-08 16:04:37.950][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-02-08 16:04:37.951][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-02-08 16:04:37.953][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-02-08 16:04:37.954][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-02-08 16:04:37.956][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-02-08 16:04:37.957][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-02-08 16:04:37.959][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-02-08 16:04:37.961][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-02-08 16:04:37.962][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-02-08 16:04:37.964][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-02-08 16:04:37.965][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-02-08 16:04:37.967][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-02-08 16:04:37.968][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-02-08 16:04:37.970][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-02-08 16:04:37.971][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-02-08 16:04:37.973][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-02-08 16:04:37.975][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-02-08 16:04:37.976][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-02-08 16:04:37.978][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-02-08 16:04:37.979][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-02-08 16:04:37.981][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-02-08 16:04:37.982][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-02-08 16:04:37.984][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-02-08 16:04:37.985][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-02-08 16:04:37.987][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-02-08 16:04:37.988][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-02-08 16:04:37.990][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-02-08 16:04:37.991][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-02-08 16:04:37.993][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-02-08 16:04:37.994][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-02-08 16:04:37.996][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-02-08 16:04:37.997][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-02-08 16:04:37.999][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-02-08 16:04:38.000][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-02-08 16:04:38.002][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-02-08 16:04:38.004][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-02-08 16:04:38.005][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-02-08 16:04:38.007][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-02-08 16:04:38.008][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-02-08 16:04:38.010][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-02-08 16:04:38.011][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-02-08 16:04:38.013][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-02-08 16:04:38.014][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-02-08 16:04:38.016][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-02-08 16:04:38.017][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-02-08 16:04:38.019][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-02-08 16:04:38.021][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-02-08 16:04:38.022][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-02-08 16:04:38.024][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-02-08 16:04:38.025][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-02-08 16:04:38.027][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-02-08 16:04:38.028][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-02-08 16:04:38.030][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-02-08 16:04:38.031][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-02-08 16:04:38.033][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-02-08 16:04:38.035][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-02-08 16:04:38.036][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-02-08 16:04:38.038][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-02-08 16:04:38.039][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-02-08 16:04:38.041][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-02-08 16:04:38.042][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-02-08 16:04:38.044][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-02-08 16:04:38.045][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-02-08 16:04:38.047][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-02-08 16:04:38.048][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-02-08 16:04:38.050][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-02-08 16:04:38.051][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-02-08 16:04:38.053][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-02-08 16:04:38.055][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-02-08 16:04:38.056][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-02-08 16:04:38.058][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-02-08 16:04:38.059][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-02-08 16:04:38.061][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-02-08 16:04:38.062][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-02-08 16:04:38.085][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-02-08 16:04:38.088][initialize] This is biodb version 1.15.0.
biodb.DEBUG[2025-02-08 16:04:38.091][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-02-08 16:04:38.092][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:04:38.093][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:04:38.094][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:04:38.095][FUN] Functions in observer BiodbConfig: [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[2025-02-08 16:04:38.100][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:04:38.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-08 16:04:38.102][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-08 16:04:38.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:04:38.104][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:04:38.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:04:38.106][FUN] Functions in observer BiodbConfig: [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[2025-02-08 16:04:38.107][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:04:38.108][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-08 16:04:38.109][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-08 16:04:38.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:04:38.112][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:04:38.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:04:38.114][FUN] Functions in observer BiodbConfig: [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[2025-02-08 16:04:38.115][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:04:38.116][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-08 16:04:38.117][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-08 16:04:38.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:04:38.119][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:04:38.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:04:38.121][FUN] Functions in observer BiodbConfig: [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[2025-02-08 16:04:38.122][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:04:38.123][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-08 16:04:38.124][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-08 16:04:38.125][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:04:38.126][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:04:38.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:04:38.155][FUN] Functions in observer BiodbConfig: [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[2025-02-08 16:04:38.156][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:04:38.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-08 16:04:38.158][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-08 16:04:38.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:04:38.160][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:04:38.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:04:38.162][FUN] Functions in observer BiodbConfig: [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[2025-02-08 16:04:38.164][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:04:38.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-08 16:04:38.166][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-08 16:04:38.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:04:38.168][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:04:38.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:04:38.170][FUN] Functions in observer BiodbConfig: [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[2025-02-08 16:04:38.171][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:04:38.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-08 16:04:38.173][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-08 16:04:38.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:04:38.175][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:04:38.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:04:38.177][FUN] Functions in observer BiodbConfig: [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[2025-02-08 16:04:38.178][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:04:38.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-08 16:04:38.180][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-08 16:04:38.181][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:04:38.182][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:04:38.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:04:38.184][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[2025-02-08 16:04:38.185][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:04:38.186][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-08 16:04:38.187][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-08 16:04:38.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:04:38.190][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:04:38.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:04:38.192][FUN] Functions in observer BiodbConfig: [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[2025-02-08 16:04:38.193][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:04:38.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-08 16:04:38.195][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-08 16:04:38.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:04:38.197][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:04:38.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:04:38.199][FUN] Functions in observer BiodbConfig: [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[2025-02-08 16:04:38.200][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:04:38.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-08 16:04:38.202][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-08 16:04:38.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:04:38.204][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:04:38.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:04:38.206][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[2025-02-08 16:04:38.207][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:04:38.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-08 16:04:38.210][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-08 16:04:38.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:04:38.212][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:04:38.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:04:38.214][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:04:38.215][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:04:38.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-08 16:04:38.217][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-08 16:04:38.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:04:38.219][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:04:38.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:04:38.221][FUN] Functions in observer BiodbConfig: [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[2025-02-08 16:04:38.222][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:04:38.223][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-08 16:04:38.225][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-08 16:04:38.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:04:38.227][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:04:38.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:04:38.229][FUN] Functions in observer BiodbConfig: [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[2025-02-08 16:04:38.230][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:04:38.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-08 16:04:38.232][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-08 16:04:38.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:04:38.234][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:04:38.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:04:38.236][FUN] Functions in observer BiodbConfig: [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[2025-02-08 16:04:38.237][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:04:38.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-08 16:04:38.239][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-08 16:04:38.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:04:38.241][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:04:38.242][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:04:38.243][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[2025-02-08 16:04:38.244][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:04:38.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-08 16:04:38.247][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-08 16:04:38.248][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:04:38.249][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:04:38.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:04:38.251][FUN] Functions in observer BiodbConfig: [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[2025-02-08 16:04:38.252][biodb$getConfig()$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-02-08 16:04:38.253][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:04:38.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-08 16:04:38.255][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-08 16:04:38.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:04:38.257][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:04:38.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:04:38.259][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:04:38.262][biodb$loadDefinitions] Load definitions from file "E:/biocbuild/bbs-3.21-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/definitions.yml".
biodb.DEBUG[2025-02-08 16:04:38.271][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2025-02-08 16:04:38.273][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-02-08 16:04:38.274][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-02-08 16:04:38.275][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-08 16:04:38.277][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-08 16:04:38.278][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-02-08 16:04:38.279][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2025-02-08 16:04:38.280][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-02-08 16:04:38.281][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-08 16:04:38.282][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-02-08 16:04:38.284][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-08 16:04:38.285][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-02-08 16:04:38.286][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2025-02-08 16:04:38.287][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-08 16:04:38.288][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2025-02-08 16:04:38.288][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2025-02-08 16:04:38.288][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2025-02-08 16:04:38.288][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2025-02-08 16:04:38.288][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2025-02-08 16:04:38.288][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2025-02-08 16:04:38.288][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2025-02-08 16:04:38.288][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2025-02-08 16:04:38.288][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2025-02-08 16:04:38.288][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2025-02-08 16:04:38.288][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2025-02-08 16:04:38.288][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2025-02-08 16:04:38.288][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2025-02-08 16:04:38.288][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2025-02-08 16:04:38.288][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2025-02-08 16:04:38.288][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2025-02-08 16:04:38.288][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2025-02-08 16:04:38.288][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2025-02-08 16:04:38.290][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-02-08 16:04:38.291][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-02-08 16:04:38.291][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2025-02-08 16:04:38.291][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2025-02-08 16:04:38.292][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-02-08 16:04:38.293][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-08 16:04:38.294][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-08 16:04:38.295][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-08 16:04:38.296][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-08 16:04:38.297][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-08 16:04:38.298][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-08 16:04:38.300][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2025-02-08 16:04:38.300][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2025-02-08 16:04:38.301][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-08 16:04:38.302][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-08 16:04:38.303][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-02-08 16:04:38.304][self$setPropertyValue]
biodb.DEBUG[2025-02-08 16:04:38.309][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2025-02-08 16:04:38.311][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-02-08 16:04:38.313][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-02-08 16:04:38.314][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-02-08 16:04:38.316][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-02-08 16:04:38.336][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2025-02-08 16:04:38.338][initialize] Register connector hmdb.metabolites with the request scheduler
biodb.DEBUG[2025-02-08 16:04:38.341][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites.
biodb.DEBUG[2025-02-08 16:04:38.345][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2025-02-08 16:04:38.348][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-02-08 16:04:38.350][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-02-08 16:04:38.351][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca".
biodb.DEBUG[2025-02-08 16:04:38.352][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.INFO [2025-02-08 16:04:38.369][biodb::testThat]
biodb.INFO [2025-02-08 16:04:38.370][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-02-08 16:04:38.371][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-08 16:04:38.372][biodb::testThat]
biodb.TRACE[2025-02-08 16:04:38.378][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[2025-02-08 16:04:38.380][biodb$getFactory()$createEntryFromCo ...] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-02-08 16:04:38.383][biodb$getFactory()$createEntryFromCo ...] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-02-08 16:04:38.390][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-08 16:04:38.391][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-08 16:04:38.392][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-08 16:04:38.408][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:04:38.409][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:04:38.410][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:04:38.411][FUN] Functions in observer BiodbConfig: [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[2025-02-08 16:04:38.421][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:04:38.422][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:04:38.423][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.424][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.426][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:04:38.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:04:38.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.441][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-02-08 16:04:38.442][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-02-08 16:04:38.443][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.444][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.467][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-02-08 16:04:38.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-02-08 16:04:38.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.472][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-02-08 16:04:38.473][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-02-08 16:04:38.474][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.475][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.477][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-02-08 16:04:38.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-02-08 16:04:38.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.482][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-08 16:04:38.483][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-08 16:04:38.484][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.485][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.487][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-08 16:04:38.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-08 16:04:38.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.492][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-08 16:04:38.493][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-08 16:04:38.494][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.495][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.497][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-08 16:04:38.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-08 16:04:38.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.501][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-02-08 16:04:38.503][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-02-08 16:04:38.504][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.505][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.506][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-02-08 16:04:38.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-02-08 16:04:38.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.511][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-08 16:04:38.512][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-08 16:04:38.513][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.515][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.516][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-08 16:04:38.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-08 16:04:38.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.521][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-08 16:04:38.522][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-08 16:04:38.523][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.524][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.526][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-08 16:04:38.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-08 16:04:38.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.531][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-02-08 16:04:38.532][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-02-08 16:04:38.533][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.534][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.536][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-02-08 16:04:38.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-02-08 16:04:38.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.542][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-02-08 16:04:38.544][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-02-08 16:04:38.545][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.554][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.556][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-02-08 16:04:38.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-02-08 16:04:38.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.561][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-08 16:04:38.562][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-08 16:04:38.563][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.564][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.565][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-08 16:04:38.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-08 16:04:38.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.570][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-08 16:04:38.572][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-08 16:04:38.573][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.574][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.575][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-08 16:04:38.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-08 16:04:38.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.580][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-08 16:04:38.582][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-08 16:04:38.583][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.584][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.585][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-08 16:04:38.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-08 16:04:38.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.590][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-08 16:04:38.591][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-08 16:04:38.593][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.594][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.595][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-08 16:04:38.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-08 16:04:38.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.600][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-08 16:04:38.601][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-08 16:04:38.602][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.603][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.605][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-08 16:04:38.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-08 16:04:38.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.610][ef$get] Asked field names are: description.
biodb.TRACE[2025-02-08 16:04:38.611][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-02-08 16:04:38.612][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.613][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.615][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-08 16:04:38.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-08 16:04:38.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.619][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-08 16:04:38.621][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-08 16:04:38.622][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.623][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.624][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-08 16:04:38.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-08 16:04:38.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.629][ef$get] Asked field names are: super.class.
biodb.TRACE[2025-02-08 16:04:38.630][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-02-08 16:04:38.632][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.633][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.634][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2025-02-08 16:04:38.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-02-08 16:04:38.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.639][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:04:38.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:04:38.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.644][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:04:38.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:04:38.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.649][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:04:38.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:04:38.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.680][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-02-08 16:04:38.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-02-08 16:04:38.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.685][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-02-08 16:04:38.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-02-08 16:04:38.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.689][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-02-08 16:04:38.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-02-08 16:04:38.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.694][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-08 16:04:38.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-08 16:04:38.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.699][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-08 16:04:38.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-08 16:04:38.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.704][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-08 16:04:38.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-08 16:04:38.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.713][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-08 16:04:38.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-08 16:04:38.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.717][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-08 16:04:38.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-08 16:04:38.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.722][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-08 16:04:38.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-08 16:04:38.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.726][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-02-08 16:04:38.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-02-08 16:04:38.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.731][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-02-08 16:04:38.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-02-08 16:04:38.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.736][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-02-08 16:04:38.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-02-08 16:04:38.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.741][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-02-08 16:04:38.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-02-08 16:04:38.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.745][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-02-08 16:04:38.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-02-08 16:04:38.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.750][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-02-08 16:04:38.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-02-08 16:04:38.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.755][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-02-08 16:04:38.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-02-08 16:04:38.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.760][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-02-08 16:04:38.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-02-08 16:04:38.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.764][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-02-08 16:04:38.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-02-08 16:04:38.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.769][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-02-08 16:04:38.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-02-08 16:04:38.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.774][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-02-08 16:04:38.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-02-08 16:04:38.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.778][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-02-08 16:04:38.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-02-08 16:04:38.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.783][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-08 16:04:38.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-08 16:04:38.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.788][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-08 16:04:38.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-08 16:04:38.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.792][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-08 16:04:38.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-08 16:04:38.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.797][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-08 16:04:38.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-08 16:04:38.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.802][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-08 16:04:38.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-08 16:04:38.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.806][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-08 16:04:38.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-08 16:04:38.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.811][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-08 16:04:38.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-08 16:04:38.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.816][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-08 16:04:38.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-08 16:04:38.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.820][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-08 16:04:38.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-08 16:04:38.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.825][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-08 16:04:38.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-08 16:04:38.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.830][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-08 16:04:38.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-08 16:04:38.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.835][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-08 16:04:38.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-08 16:04:38.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.839][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-08 16:04:38.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-08 16:04:38.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.844][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-08 16:04:38.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-08 16:04:38.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.849][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-08 16:04:38.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-08 16:04:38.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.853][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-08 16:04:38.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-08 16:04:38.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.858][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-08 16:04:38.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-08 16:04:38.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.863][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-08 16:04:38.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-08 16:04:38.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.867][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-08 16:04:38.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-08 16:04:38.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.872][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-08 16:04:38.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-08 16:04:38.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.877][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-08 16:04:38.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-08 16:04:38.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.881][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-08 16:04:38.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-08 16:04:38.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.891][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-08 16:04:38.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-08 16:04:38.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.895][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-08 16:04:38.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-08 16:04:38.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.900][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-02-08 16:04:38.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-02-08 16:04:38.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.905][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-02-08 16:04:38.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-02-08 16:04:38.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.910][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-02-08 16:04:38.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-02-08 16:04:38.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.914][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-08 16:04:38.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-08 16:04:38.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.919][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-08 16:04:38.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-08 16:04:38.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.924][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-08 16:04:38.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-08 16:04:38.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.929][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-02-08 16:04:38.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-08 16:04:38.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.933][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-08 16:04:38.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-08 16:04:38.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.938][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-08 16:04:38.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-08 16:04:38.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.943][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-08 16:04:38.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-08 16:04:38.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.948][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-02-08 16:04:38.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-08 16:04:38.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.967][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-08 16:04:38.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-08 16:04:38.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.972][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-08 16:04:38.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-08 16:04:38.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.977][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-08 16:04:38.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-08 16:04:38.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.982][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-08 16:04:38.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-08 16:04:38.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.986][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-08 16:04:38.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-08 16:04:38.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.991][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-02-08 16:04:38.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-02-08 16:04:38.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:38.996][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-02-08 16:04:38.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-02-08 16:04:38.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:38.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.001][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:04:39.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:04:39.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.005][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-02-08 16:04:39.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-02-08 16:04:39.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.010][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:04:39.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:04:39.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.015][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:04:39.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:04:39.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.019][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:04:39.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:04:39.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.024][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:04:39.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:04:39.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.029][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:04:39.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:04:39.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.034][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:04:39.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:04:39.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-08 16:04:39.038][biodb$getFactory()$createEntryFromCo ...] Accession numbers: HMDB0000001.
biodb.TRACE[2025-02-08 16:04:39.042][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-02-08 16:04:39.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-02-08 16:04:39.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.046][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-02-08 16:04:39.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-02-08 16:04:39.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.051][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-02-08 16:04:39.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-02-08 16:04:39.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.060][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-02-08 16:04:39.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-02-08 16:04:39.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.085][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:04:39.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:04:39.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.103][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-02-08 16:04:39.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-02-08 16:04:39.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.114][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:04:39.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:04:39.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.118][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:04:39.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:04:39.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.123][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:04:39.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:04:39.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.129][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:04:39.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:04:39.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.134][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:04:39.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:04:39.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.139][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:04:39.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:04:39.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.143][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-02-08 16:04:39.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-02-08 16:04:39.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.148][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-02-08 16:04:39.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-02-08 16:04:39.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.153][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-02-08 16:04:39.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-02-08 16:04:39.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.167][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:04:39.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:04:39.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.172][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:04:39.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:04:39.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.176][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:04:39.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:04:39.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.181][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:04:39.183][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:04:39.184][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.185][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.186][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:04:39.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:04:39.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.201][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-02-08 16:04:39.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-02-08 16:04:39.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.206][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-02-08 16:04:39.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-02-08 16:04:39.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.211][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-02-08 16:04:39.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-02-08 16:04:39.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.215][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-02-08 16:04:39.217][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-02-08 16:04:39.218][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.219][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.220][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-02-08 16:04:39.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-02-08 16:04:39.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.234][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-02-08 16:04:39.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-02-08 16:04:39.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.239][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-02-08 16:04:39.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-02-08 16:04:39.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.249][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-02-08 16:04:39.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-02-08 16:04:39.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.254][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-02-08 16:04:39.255][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-02-08 16:04:39.256][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.258][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.259][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-02-08 16:04:39.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-02-08 16:04:39.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.273][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-08 16:04:39.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-08 16:04:39.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.278][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-08 16:04:39.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-08 16:04:39.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.283][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-08 16:04:39.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-08 16:04:39.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.287][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-08 16:04:39.289][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-08 16:04:39.290][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.291][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.292][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-08 16:04:39.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-08 16:04:39.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.307][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-08 16:04:39.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-08 16:04:39.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.311][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-08 16:04:39.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-08 16:04:39.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.316][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-08 16:04:39.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-08 16:04:39.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.321][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-08 16:04:39.322][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-08 16:04:39.323][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.325][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.326][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-08 16:04:39.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-08 16:04:39.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.340][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-08 16:04:39.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-08 16:04:39.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.345][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-08 16:04:39.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-08 16:04:39.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.350][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-08 16:04:39.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-08 16:04:39.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.354][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-08 16:04:39.356][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-08 16:04:39.357][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.358][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.359][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-08 16:04:39.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-08 16:04:39.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.374][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-08 16:04:39.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-08 16:04:39.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.379][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-08 16:04:39.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-08 16:04:39.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.383][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-08 16:04:39.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-08 16:04:39.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.388][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-08 16:04:39.389][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-08 16:04:39.390][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.392][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.393][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-08 16:04:39.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-08 16:04:39.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.408][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-08 16:04:39.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-08 16:04:39.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.412][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-08 16:04:39.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-08 16:04:39.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.417][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-08 16:04:39.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-08 16:04:39.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.422][ef$get] Asked field names are: description.
biodb.TRACE[2025-02-08 16:04:39.423][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-02-08 16:04:39.424][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.425][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.431][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-02-08 16:04:39.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-02-08 16:04:39.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.446][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-08 16:04:39.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-08 16:04:39.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.453][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-08 16:04:39.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-08 16:04:39.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.460][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-08 16:04:39.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-08 16:04:39.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.467][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-08 16:04:39.469][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-08 16:04:39.470][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.472][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.474][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-08 16:04:39.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-08 16:04:39.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.492][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-02-08 16:04:39.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-02-08 16:04:39.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.497][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-02-08 16:04:39.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-02-08 16:04:39.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.501][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-02-08 16:04:39.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-02-08 16:04:39.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.506][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-02-08 16:04:39.507][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-02-08 16:04:39.508][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.510][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.511][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-02-08 16:04:39.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-02-08 16:04:39.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.525][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-08 16:04:39.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-08 16:04:39.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.530][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-08 16:04:39.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-08 16:04:39.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.535][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-08 16:04:39.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-08 16:04:39.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.540][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-08 16:04:39.541][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-08 16:04:39.542][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.543][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.545][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-08 16:04:39.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-08 16:04:39.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.559][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-02-08 16:04:39.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-02-08 16:04:39.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.564][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-02-08 16:04:39.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-02-08 16:04:39.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.569][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-02-08 16:04:39.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-02-08 16:04:39.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.574][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-02-08 16:04:39.575][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-02-08 16:04:39.576][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.577][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.578][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-02-08 16:04:39.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-02-08 16:04:39.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.593][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-02-08 16:04:39.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-02-08 16:04:39.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.598][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-02-08 16:04:39.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-02-08 16:04:39.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.603][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-02-08 16:04:39.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-02-08 16:04:39.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.607][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-02-08 16:04:39.609][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-02-08 16:04:39.610][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.611][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.612][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-02-08 16:04:39.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-02-08 16:04:39.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.632][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-02-08 16:04:39.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-02-08 16:04:39.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.637][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-02-08 16:04:39.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-02-08 16:04:39.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.642][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-02-08 16:04:39.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-02-08 16:04:39.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.646][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-02-08 16:04:39.648][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-02-08 16:04:39.649][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.650][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.651][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-02-08 16:04:39.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-02-08 16:04:39.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.666][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-08 16:04:39.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-08 16:04:39.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.671][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-08 16:04:39.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-08 16:04:39.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.676][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-08 16:04:39.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-08 16:04:39.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.681][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-08 16:04:39.682][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-08 16:04:39.683][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.684][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.686][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-02-08 16:04:39.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-08 16:04:39.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.700][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-08 16:04:39.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-08 16:04:39.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.705][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-08 16:04:39.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-08 16:04:39.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.710][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-08 16:04:39.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-08 16:04:39.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.715][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-08 16:04:39.716][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-08 16:04:39.717][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.718][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.719][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-08 16:04:39.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-08 16:04:39.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.734][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-08 16:04:39.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-08 16:04:39.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.739][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-08 16:04:39.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-08 16:04:39.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.744][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-08 16:04:39.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-08 16:04:39.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.748][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-08 16:04:39.750][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-08 16:04:39.751][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.752][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.753][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-08 16:04:39.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-08 16:04:39.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.767][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-08 16:04:39.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-08 16:04:39.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.772][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-08 16:04:39.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-08 16:04:39.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.777][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-08 16:04:39.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-08 16:04:39.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.782][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-08 16:04:39.783][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-08 16:04:39.784][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.785][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.787][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-08 16:04:39.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-08 16:04:39.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.801][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:04:39.802][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:04:39.803][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.805][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.816][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-02-08 16:04:39.817][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-02-08 16:04:39.819][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.820][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.826][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-08 16:04:39.828][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-08 16:04:39.829][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.830][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.837][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-02-08 16:04:39.838][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-02-08 16:04:39.839][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.840][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.847][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-02-08 16:04:39.849][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-02-08 16:04:39.850][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.851][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.858][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-02-08 16:04:39.859][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-02-08 16:04:39.860][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.861][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.868][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-02-08 16:04:39.869][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-02-08 16:04:39.870][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.871][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.878][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-02-08 16:04:39.879][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-02-08 16:04:39.880][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.881][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.888][ef$get] Asked field names are: description.
biodb.TRACE[2025-02-08 16:04:39.889][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-02-08 16:04:39.890][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.892][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.898][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-08 16:04:39.899][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-08 16:04:39.900][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.902][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.908][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-08 16:04:39.909][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-08 16:04:39.910][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.912][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.918][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-08 16:04:39.919][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-08 16:04:39.920][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.922][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.928][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-02-08 16:04:39.929][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-02-08 16:04:39.930][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.931][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.938][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-02-08 16:04:39.939][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-02-08 16:04:39.940][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.941][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.948][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-08 16:04:39.949][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-08 16:04:39.950][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.951][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.958][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-08 16:04:39.959][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-02-08 16:04:39.960][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.961][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.967][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-02-08 16:04:39.969][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-02-08 16:04:39.970][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.971][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:04:39.977][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-02-08 16:04:39.979][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-02-08 16:04:39.980][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:04:39.981][ef$get] fields variable is a list.
biodb.INFO [2025-02-08 16:04:39.993][biodb::testThat]
biodb.INFO [2025-02-08 16:04:39.994][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-02-08 16:04:39.995][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-08 16:04:39.996][biodb::testThat]
biodb.DEBUG[2025-02-08 16:04:40.013][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-02-08 16:04:40.019][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.INFO [2025-02-08 16:04:40.025][self$getFolderPath] Create cache folder "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34" for "hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34".
biodb.DEBUG[2025-02-08 16:04:40.027][self$isDownloaded] Database hmdb.metabolites has not yet been downloaded.
biodb.INFO [2025-02-08 16:04:40.028][self$download] Downloading whole database of hmdb.metabolites.
biodb.INFO [2025-02-08 16:04:40.030][private$doDownload] Downloading HMDB metabolite database at "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip" ...
biodb.DEBUG[2025-02-08 16:04:40.032][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 62.3 MB

biodb.INFO [2025-02-08 16:05:53.827][biodb::testThat]
biodb.INFO [2025-02-08 16:05:53.829][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-02-08 16:05:53.830][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-08 16:05:53.831][biodb::testThat]
biodb.TRACE[2025-02-08 16:05:53.835][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-08 16:05:53.836][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-08 16:05:53.837][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:53.838][ef$get] fields variable is a list.
biodb.DEBUG[2025-02-08 16:05:53.840][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "name".
biodb.DEBUG[2025-02-08 16:05:53.863][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-02-08 16:05:53.909][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-02-08 16:05:53.912][self$isDownloaded] Database hmdb.metabolites has not yet been downloaded.
biodb.INFO [2025-02-08 16:05:53.913][self$download] Downloading whole database of hmdb.metabolites.
biodb.INFO [2025-02-08 16:05:53.914][private$doDownload] Downloading HMDB metabolite database at "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip" ...
biodb.DEBUG[2025-02-08 16:05:53.928][sched$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 440.7 MB

biodb.INFO [2025-02-08 16:07:08.299][biodb::testThat]
biodb.INFO [2025-02-08 16:07:08.301][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-02-08 16:07:08.302][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-08 16:07:08.303][biodb::testThat]
biodb.DEBUG[2025-02-08 16:07:08.313][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-02-08 16:07:08.314][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-02-08 16:07:08.317][self$isDownloaded] Database hmdb.metabolites has not yet been downloaded.
biodb.INFO [2025-02-08 16:07:08.318][self$download] Downloading whole database of hmdb.metabolites.
biodb.INFO [2025-02-08 16:07:08.319][private$doDownload] Downloading HMDB metabolite database at "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip" ...
biodb.DEBUG[2025-02-08 16:07:08.321][sched$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 207.1 MB

biodb.INFO [2025-02-08 16:08:12.169][biodb::testThat]
biodb.INFO [2025-02-08 16:08:12.170][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-02-08 16:08:12.171][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-08 16:08:12.172][biodb::testThat]
biodb.DEBUG[2025-02-08 16:08:12.177][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-02-08 16:08:12.178][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-02-08 16:08:12.181][self$isDownloaded] Database hmdb.metabolites has not yet been downloaded.
biodb.INFO [2025-02-08 16:08:12.182][self$download] Downloading whole database of hmdb.metabolites.
biodb.INFO [2025-02-08 16:08:12.183][private$doDownload] Downloading HMDB metabolite database at "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip" ...
biodb.DEBUG[2025-02-08 16:08:12.186][sched$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 16.5 MB

biodb.INFO [2025-02-08 16:08:40.737][biodb::testThat]
biodb.INFO [2025-02-08 16:08:40.738][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-02-08 16:08:40.739][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-08 16:08:40.740][biodb::testThat]
biodb.INFO [2025-02-08 16:08:40.751][biodb::testThat]
biodb.INFO [2025-02-08 16:08:40.753][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-02-08 16:08:40.754][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-08 16:08:40.755][biodb::testThat]
biodb.INFO [2025-02-08 16:08:40.766][biodb::testThat]
biodb.INFO [2025-02-08 16:08:40.767][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-02-08 16:08:40.768][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-08 16:08:40.769][biodb::testThat]
biodb.DEBUG[2025-02-08 16:08:40.774][function(conn, opt)] Trying to download "http://www.hmdb.ca/metabolites/HMDB0000001".
biodb.DEBUG[2025-02-08 16:09:15.684][getUrlContent] Use base::url() for downloading content of URL http://www.hmdb.ca/metabolites/HMDB0000001.
biodb.INFO [2025-02-08 16:09:25.392][biodb::testThat]
biodb.INFO [2025-02-08 16:09:25.393][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-02-08 16:09:25.394][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-08 16:09:25.395][biodb::testThat]
biodb.DEBUG[2025-02-08 16:09:25.723][getUrlContent] Use base::url() for downloading content of URL http://www.hmdb.ca/structures/HMDB0000001/image.png.
biodb.TRACE[2025-02-08 16:09:26.364][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-08 16:09:26.366][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-08 16:09:26.367][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:09:26.368][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:09:26.370][ef$get] Asked field names are: description.
biodb.TRACE[2025-02-08 16:09:26.371][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-02-08 16:09:26.372][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:09:26.373][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:09:26.374][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-02-08 16:09:26.376][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-02-08 16:09:26.377][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:09:26.378][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:09:26.379][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-08 16:09:26.381][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-08 16:09:26.382][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:09:26.383][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:09:26.389][ef$get] Asked field names are: description.
biodb.TRACE[2025-02-08 16:09:26.391][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-02-08 16:09:26.392][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:09:26.393][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:09:26.395][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-02-08 16:09:26.396][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-02-08 16:09:26.397][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:09:26.398][ef$get] fields variable is a list.
biodb.INFO [2025-02-08 16:09:26.399][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-02-08 16:09:26.401][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler
biodb.INFO [2025-02-08 16:09:26.402][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2025-02-08 16:09:26.403][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-02-08 16:09:26.404][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-08 16:09:26.405][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-08 16:09:26.406][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:09:26.407][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:09:26.409][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:09:26.410][FUN] Functions in observer 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 8 | 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 `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$downloadFile(url = zip.url, dest.file = tmpFile)
 10.                 └─utils::download.file(...)
── Error ('test_long_100_generic.R:42:1'): We can load an entry from the database. ──
Error in `utils::download.file(url = url, destfile = dest.file, mode = "wb", 
    method = "auto", cacheOK = FALSE, quiet = FALSE)`: download from 'http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip' failed
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
  3.   └─opt$refEntries$getRealEntry(id)
  4.     └─self$getRealEntries(ids = id)
  5.       └─private$bdb$getFactory()$getEntry(...)
  6.         └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  7.           └─conn$getEntryContent(ids)
  8.             └─self$download()
  9.               └─private$doDownload()
 10.                 └─sched$downloadFile(url = zip.url, dest.file = tmpFile)
 11.                   └─utils::download.file(...)

[ FAIL 4 | WARN 8 | 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_1.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbuild/bbs-3.21-bioc-longtests/meat/biodbHmdb.Rcheck'
* using R Under development (unstable) (2025-01-21 r87610 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* 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 '1.13.0'
* 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) 13.3.0'
* 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:
    1. ├─base::do.call(fct, params)
    2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
    3.   └─opt$refEntries$getRealEntry(id)
    4.     └─self$getRealEntries(ids = id)
    5.       └─private$bdb$getFactory()$getEntry(...)
    6.         └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
    7.           └─conn$getEntryContent(ids)
    8.             └─self$download()
    9.               └─private$doDownload()
   10.                 └─sched$downloadFile(url = zip.url, dest.file = tmpFile)
   11.                   └─utils::download.file(...)
  
  [ FAIL 4 | WARN 8 | 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 '1.13.0'
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 13.3.0'
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:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -DR_NO_REMAP -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:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -DR_NO_REMAP -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:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -DR_NO_REMAP -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:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -DR_NO_REMAP -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:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -DR_NO_REMAP -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:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -DR_NO_REMAP -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:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -DR_NO_REMAP -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:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -DR_NO_REMAP -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:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -DR_NO_REMAP -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:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -DR_NO_REMAP -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:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -DR_NO_REMAP -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:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/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)