Back to Long Tests report for BioC 3.21

This page was generated on 2025-09-06 23:55 -0400 (Sat, 06 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4606
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 7/30HostnameOS / ArchCHECK
biodbHmdb 1.14.0  (landing page)
Pierrick Roger
Snapshot Date: 2025-09-06 09:55 -0400 (Sat, 06 Sep 2025)
git_url: https://git.bioconductor.org/packages/biodbHmdb
git_branch: RELEASE_3_21
git_last_commit: a7f0a0f
git_last_commit_date: 2025-04-15 12:42:50 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  ERROR  
merida1macOS 12.7.5 Monterey / x86_64  ERROR  

CHECK results for biodbHmdb on nebbiolo1

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

raw results


Summary

Package: biodbHmdb
Version: 1.14.0
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbHmdb_1.14.0.tar.gz
StartedAt: 2025-09-06 16:01:58 -0400 (Sat, 06 Sep 2025)
EndedAt: 2025-09-06 16:03:05 -0400 (Sat, 06 Sep 2025)
EllapsedTime: 67.0 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbHmdb.Rcheck
Warnings: NA

Tests output

biodbHmdb.Rcheck/tests/testthat.Rout.fail


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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 [2025-09-06 16:03:00.169][biodb::testContext]
biodb.INFO [2025-09-06 16:03:00.171][biodb::testContext] ********************************************************************************
biodb.INFO [2025-09-06 16:03:00.172][biodb::testContext] Test context - Generic long tests
biodb.INFO [2025-09-06 16:03:00.173][biodb::testContext] ********************************************************************************
biodb.INFO [2025-09-06 16:03:00.174][biodb::testContext]
biodb.INFO [2025-09-06 16:03:00.179][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.16.0.
biodb.DEBUG[2025-09-06 16:03:00.181][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-09-06 16:03:00.188][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-09-06 16:03:00.189][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-09-06 16:03:00.190][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-09-06 16:03:00.190][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:00.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:00.192][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:00.193][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-09-06 16:03:00.210][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-09-06 16:03:00.211][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:00.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:00.212][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:00.213][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-09-06 16:03:00.214][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-09-06 16:03:00.215][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:00.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:00.217][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:00.218][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-09-06 16:03:00.219][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-09-06 16:03:00.219][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-09-06 16:03:00.220][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:00.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:00.222][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:00.223][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-09-06 16:03:00.224][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-09-06 16:03:00.225][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-09-06 16:03:00.226][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:00.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:00.227][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:00.228][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-09-06 16:03:00.229][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-09-06 16:03:00.230][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:00.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:00.232][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:00.233][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-09-06 16:03:00.234][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-09-06 16:03:00.235][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-09-06 16:03:00.235][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:00.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:00.237][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:00.238][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-09-06 16:03:00.239][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-09-06 16:03:00.240][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:00.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:00.241][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:00.242][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-09-06 16:03:00.243][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-09-06 16:03:00.244][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-09-06 16:03:00.245][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:00.246][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:00.247][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:00.248][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-09-06 16:03:00.249][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-09-06 16:03:00.250][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-09-06 16:03:00.250][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-09-06 16:03:00.251][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-09-06 16:03:00.252][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-09-06 16:03:00.253][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:00.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:00.255][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:00.256][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-09-06 16:03:00.257][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-09-06 16:03:00.258][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:00.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:00.259][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:00.260][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-09-06 16:03:00.261][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-09-06 16:03:00.262][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:00.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:00.264][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:00.265][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-09-06 16:03:00.266][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-09-06 16:03:00.266][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:00.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:00.268][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:00.269][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-09-06 16:03:00.270][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-09-06 16:03:00.271][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:00.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:00.272][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:00.273][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-09-06 16:03:00.274][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-09-06 16:03:00.275][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:00.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:00.277][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:00.278][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-09-06 16:03:00.279][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-09-06 16:03:00.284][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-09-06 16:03:00.285][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:00.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:00.286][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:00.287][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-09-06 16:03:00.288][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-09-06 16:03:00.289][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-09-06 16:03:00.290][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:00.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:00.292][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:00.295][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-09-06 16:03:00.330][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-09-06 16:03:00.344][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-09-06 16:03:00.345][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-06 16:03:00.346][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-06 16:03:00.347][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-06 16:03:00.348][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-06 16:03:00.349][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-06 16:03:00.350][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-06 16:03:00.351][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-09-06 16:03:00.352][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-06 16:03:00.353][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-09-06 16:03:00.353][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-09-06 16:03:00.354][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-06 16:03:00.355][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-06 16:03:00.356][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-06 16:03:00.357][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-09-06 16:03:00.357][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-09-06 16:03:00.357][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-09-06 16:03:00.357][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-09-06 16:03:00.357][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-09-06 16:03:00.358][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-06 16:03:00.359][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:03:00.360][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:03:00.361][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-06 16:03:00.362][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:03:00.363][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:03:00.364][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-06 16:03:00.365][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-06 16:03:00.365][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-06 16:03:00.366][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-06 16:03:00.367][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-06 16:03:00.368][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-06 16:03:00.369][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-09-06 16:03:00.371][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-09-06 16:03:00.372][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-09-06 16:03:00.373][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-06 16:03:00.374][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-06 16:03:00.375][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-06 16:03:00.376][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-06 16:03:00.376][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-06 16:03:00.377][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-06 16:03:00.378][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-09-06 16:03:00.379][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-06 16:03:00.380][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-09-06 16:03:00.381][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-09-06 16:03:00.382][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-06 16:03:00.383][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-06 16:03:00.384][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-06 16:03:00.385][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-09-06 16:03:00.385][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-09-06 16:03:00.385][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-09-06 16:03:00.385][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-09-06 16:03:00.385][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-09-06 16:03:00.386][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-06 16:03:00.387][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:03:00.388][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:03:00.389][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-06 16:03:00.390][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:03:00.390][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:03:00.391][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-06 16:03:00.392][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-06 16:03:00.393][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-06 16:03:00.394][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-06 16:03:00.395][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-06 16:03:00.396][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-06 16:03:00.397][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-09-06 16:03:00.398][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-09-06 16:03:00.399][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-09-06 16:03:00.400][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-06 16:03:00.401][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-06 16:03:00.402][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-06 16:03:00.403][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-06 16:03:00.404][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-06 16:03:00.405][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-06 16:03:00.406][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-09-06 16:03:00.407][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-06 16:03:00.408][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-09-06 16:03:00.409][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-09-06 16:03:00.410][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-06 16:03:00.411][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-06 16:03:00.412][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-06 16:03:00.413][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-09-06 16:03:00.414][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-06 16:03:00.414][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:03:00.415][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:03:00.416][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-06 16:03:00.417][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:03:00.418][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:03:00.419][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-06 16:03:00.420][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-06 16:03:00.421][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-06 16:03:00.422][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-06 16:03:00.422][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-06 16:03:00.423][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-06 16:03:00.424][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-09-06 16:03:00.426][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-09-06 16:03:00.427][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-09-06 16:03:00.428][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-06 16:03:00.429][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-06 16:03:00.430][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-09-06 16:03:00.431][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-09-06 16:03:00.432][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-09-06 16:03:00.433][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-06 16:03:00.434][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-09-06 16:03:00.434][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-06 16:03:00.435][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-09-06 16:03:00.436][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-09-06 16:03:00.437][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-06 16:03:00.438][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-09-06 16:03:00.439][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-09-06 16:03:00.440][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-09-06 16:03:00.441][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-09-06 16:03:00.442][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:03:00.443][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:03:00.444][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-06 16:03:00.445][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:03:00.445][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:03:00.446][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-06 16:03:00.447][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-09-06 16:03:00.448][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-06 16:03:00.449][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-06 16:03:00.450][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-09-06 16:03:00.451][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-06 16:03:00.454][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-09-06 16:03:00.455][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:00.456][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:00.457][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:00.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:00.459][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:00.459][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:00.460][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:00.461][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:00.462][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:00.463][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:00.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:00.464][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:00.465][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:00.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:00.467][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:00.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:00.469][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:00.470][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:00.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:00.471][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:00.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:00.473][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:00.474][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:00.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:00.475][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:00.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:00.477][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:00.478][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:00.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:00.480][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:00.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:00.481][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:00.482][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:00.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:00.484][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:00.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:00.485][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:00.486][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:00.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:00.488][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:00.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:00.490][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:00.491][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:00.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:00.496][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:00.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:00.497][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:00.498][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:00.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:00.500][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:00.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:00.501][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:00.502][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:00.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:00.504][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:00.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:00.506][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:00.506][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:00.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:00.508][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:00.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:00.510][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:00.511][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:00.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:00.512][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:00.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:00.514][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:00.515][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:00.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:00.516][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:00.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:00.518][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:00.519][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:00.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:00.521][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:00.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:00.522][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:00.523][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:00.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:00.525][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:00.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:00.527][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:00.527][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:00.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:00.529][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:00.530][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:00.531][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[2025-09-06 16:03:00.532][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-09-06 16:03:00.536][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-09-06 16:03:00.537][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-09-06 16:03:00.539][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-09-06 16:03:00.540][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-09-06 16:03:00.541][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-09-06 16:03:00.542][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-09-06 16:03:00.544][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-09-06 16:03:00.545][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-09-06 16:03:00.546][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-09-06 16:03:00.548][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-09-06 16:03:00.549][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-09-06 16:03:00.550][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-09-06 16:03:00.552][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-09-06 16:03:00.553][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-09-06 16:03:00.554][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-09-06 16:03:00.556][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-09-06 16:03:00.557][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-09-06 16:03:00.558][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-09-06 16:03:00.559][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-09-06 16:03:00.561][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-09-06 16:03:00.562][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-09-06 16:03:00.563][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-09-06 16:03:00.565][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-09-06 16:03:00.566][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-09-06 16:03:00.567][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-09-06 16:03:00.569][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-09-06 16:03:00.570][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-09-06 16:03:00.571][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-09-06 16:03:00.573][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-09-06 16:03:00.574][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-09-06 16:03:00.575][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-09-06 16:03:00.576][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-09-06 16:03:00.578][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-09-06 16:03:00.579][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-09-06 16:03:00.580][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-09-06 16:03:00.582][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-09-06 16:03:00.583][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-09-06 16:03:00.584][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-09-06 16:03:00.585][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-09-06 16:03:00.587][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-09-06 16:03:00.588][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-09-06 16:03:00.589][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-09-06 16:03:00.591][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-09-06 16:03:00.592][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-09-06 16:03:00.593][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-09-06 16:03:00.595][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-09-06 16:03:00.596][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-09-06 16:03:00.597][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-09-06 16:03:00.599][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-09-06 16:03:00.600][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-09-06 16:03:00.601][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-09-06 16:03:00.602][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-09-06 16:03:00.604][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-09-06 16:03:00.605][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-09-06 16:03:00.606][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-09-06 16:03:00.608][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-09-06 16:03:00.609][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-09-06 16:03:00.610][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-09-06 16:03:00.617][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-09-06 16:03:00.619][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-09-06 16:03:00.621][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-09-06 16:03:00.622][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-09-06 16:03:00.624][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-09-06 16:03:00.625][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-09-06 16:03:00.627][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-09-06 16:03:00.628][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-09-06 16:03:00.630][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-09-06 16:03:00.631][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-09-06 16:03:00.633][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-09-06 16:03:00.634][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-09-06 16:03:00.636][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-09-06 16:03:00.637][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-09-06 16:03:00.639][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-09-06 16:03:00.640][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-09-06 16:03:00.642][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-09-06 16:03:00.643][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-09-06 16:03:00.644][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-09-06 16:03:00.646][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-09-06 16:03:00.647][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-09-06 16:03:00.649][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-09-06 16:03:00.650][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-09-06 16:03:00.652][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-09-06 16:03:00.659][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-09-06 16:03:00.661][initialize] This is biodb version 1.16.0.
biodb.DEBUG[2025-09-06 16:03:00.664][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-09-06 16:03:00.665][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:00.666][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:00.667][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:00.668][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:00.686][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:00.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:03:00.688][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:03:00.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:00.690][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:00.691][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:00.692][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:00.693][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:00.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:03:00.695][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:03:00.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:00.697][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:00.697][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:00.698][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:00.699][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:00.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:03:00.701][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:03:00.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:00.703][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:00.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:00.705][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:00.706][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:00.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:03:00.708][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:03:00.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:00.710][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:00.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:00.712][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:00.713][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:00.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:03:00.714][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:03:00.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:00.716][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:00.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:00.718][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:00.719][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:00.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:03:00.721][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:03:00.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:00.723][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:00.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:00.725][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:00.726][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:00.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:03:00.727][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:03:00.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:00.729][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:00.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:00.731][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:00.732][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:00.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:03:00.734][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:03:00.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:00.736][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:00.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:00.737][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:00.738][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:00.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:03:00.740][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:03:00.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:00.742][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:00.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:00.744][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:00.745][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:00.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:03:00.747][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:03:00.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:00.748][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:00.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:00.750][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:00.751][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:00.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:03:00.753][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:03:00.754][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:00.755][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:00.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:00.757][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:00.757][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:00.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:03:00.759][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:03:00.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:00.761][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:00.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:00.763][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:00.764][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:00.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:03:00.766][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:03:00.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:00.767][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:00.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:00.769][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:00.770][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:00.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:03:00.772][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:03:00.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:00.774][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:00.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:00.776][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:00.777][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:00.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:03:00.778][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:03:00.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:00.780][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:00.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:00.782][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:00.783][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:00.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:03:00.785][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:03:00.786][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:00.786][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:00.787][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:00.788][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:00.789][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:00.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:03:00.791][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:03:00.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:00.793][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:00.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:00.795][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:00.796][biodb$getConfig()$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-09-06 16:03:00.797][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-09-06 16:03:00.797][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:03:00.798][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:03:00.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:00.800][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:00.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:00.802][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-09-06 16:03:00.804][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.21-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/definitions.yml".
biodb.DEBUG[2025-09-06 16:03:00.813][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2025-09-06 16:03:00.815][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-09-06 16:03:00.816][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-09-06 16:03:00.817][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-09-06 16:03:00.817][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-09-06 16:03:00.818][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-09-06 16:03:00.819][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2025-09-06 16:03:00.820][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-09-06 16:03:00.821][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-09-06 16:03:00.822][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-09-06 16:03:00.823][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-09-06 16:03:00.824][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-09-06 16:03:00.825][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2025-09-06 16:03:00.826][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-09-06 16:03:00.827][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2025-09-06 16:03:00.827][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2025-09-06 16:03:00.827][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2025-09-06 16:03:00.827][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2025-09-06 16:03:00.827][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2025-09-06 16:03:00.827][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2025-09-06 16:03:00.827][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2025-09-06 16:03:00.827][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2025-09-06 16:03:00.827][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2025-09-06 16:03:00.827][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2025-09-06 16:03:00.827][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2025-09-06 16:03:00.827][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2025-09-06 16:03:00.827][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2025-09-06 16:03:00.827][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2025-09-06 16:03:00.827][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2025-09-06 16:03:00.827][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2025-09-06 16:03:00.827][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2025-09-06 16:03:00.827][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2025-09-06 16:03:00.828][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-09-06 16:03:00.829][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-09-06 16:03:00.829][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2025-09-06 16:03:00.829][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2025-09-06 16:03:00.830][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-09-06 16:03:00.831][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:03:00.832][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:03:00.833][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-09-06 16:03:00.834][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-09-06 16:03:00.834][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-09-06 16:03:00.835][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-09-06 16:03:00.836][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2025-09-06 16:03:00.836][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2025-09-06 16:03:00.837][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-09-06 16:03:00.838][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-09-06 16:03:00.839][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-09-06 16:03:00.840][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-09-06 16:03:00.845][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2025-09-06 16:03:00.847][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-09-06 16:03:00.848][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-09-06 16:03:00.850][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-09-06 16:03:00.851][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-09-06 16:03:00.894][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2025-09-06 16:03:00.895][initialize] Register connector hmdb.metabolites with the request scheduler
biodb.DEBUG[2025-09-06 16:03:00.899][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites.
biodb.DEBUG[2025-09-06 16:03:00.902][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2025-09-06 16:03:00.906][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-09-06 16:03:00.907][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-09-06 16:03:00.908][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca".
biodb.DEBUG[2025-09-06 16:03:00.909][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.INFO [2025-09-06 16:03:00.917][biodb::testThat]
biodb.INFO [2025-09-06 16:03:00.918][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-09-06 16:03:00.919][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-06 16:03:00.920][biodb::testThat]
biodb.TRACE[2025-09-06 16:03:00.923][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.21-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/testref/entry-hmdb.metabolites-HMDB0000001-content.xml".
biodb.DEBUG[2025-09-06 16:03:00.925][biodb$getFactory()$createEntryFromCo ...] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-09-06 16:03:00.928][biodb$getFactory()$createEntryFromCo ...] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-09-06 16:03:00.935][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-09-06 16:03:00.936][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:03:00.937][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:03:00.948][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:00.949][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:00.950][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:00.950][FUN] Functions in observer BiodbConfig: [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[2025-09-06 16:03:00.961][ef$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:03:00.962][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:03:00.963][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:00.964][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:00.965][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:03:00.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:03:00.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:00.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:00.980][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-06 16:03:00.981][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-06 16:03:00.982][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:00.983][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.007][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-06 16:03:01.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-06 16:03:01.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.011][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-09-06 16:03:01.012][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-09-06 16:03:01.013][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.014][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.015][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-09-06 16:03:01.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-09-06 16:03:01.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.019][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-06 16:03:01.020][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-06 16:03:01.021][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.022][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.023][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-06 16:03:01.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-06 16:03:01.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.027][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-06 16:03:01.028][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-06 16:03:01.028][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.029][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.031][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-06 16:03:01.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-06 16:03:01.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.034][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-09-06 16:03:01.035][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-09-06 16:03:01.036][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.037][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.038][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-09-06 16:03:01.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-09-06 16:03:01.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.042][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-06 16:03:01.043][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-06 16:03:01.044][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.045][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.046][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-06 16:03:01.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-06 16:03:01.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.050][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:03:01.051][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:03:01.052][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.061][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.062][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:03:01.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:03:01.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.066][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:03:01.067][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:03:01.068][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.069][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.070][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:03:01.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:03:01.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.074][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:03:01.075][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:03:01.075][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.076][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.077][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:03:01.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:03:01.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.081][ef$get] Asked field names are: formula.
biodb.TRACE[2025-09-06 16:03:01.082][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-06 16:03:01.083][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.084][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.085][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-06 16:03:01.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-06 16:03:01.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.089][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-09-06 16:03:01.090][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-06 16:03:01.091][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.092][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.093][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-06 16:03:01.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-06 16:03:01.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.097][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-06 16:03:01.098][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-06 16:03:01.099][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.100][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.101][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-06 16:03:01.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-06 16:03:01.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.105][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:03:01.106][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:03:01.106][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.107][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.109][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:03:01.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:03:01.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.112][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:03:01.113][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:03:01.114][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.115][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.116][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:03:01.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:03:01.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.120][ef$get] Asked field names are: description.
biodb.TRACE[2025-09-06 16:03:01.121][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-09-06 16:03:01.122][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.123][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.124][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-09-06 16:03:01.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-09-06 16:03:01.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.128][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-09-06 16:03:01.129][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-06 16:03:01.130][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.130][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.132][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-09-06 16:03:01.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-06 16:03:01.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.135][ef$get] Asked field names are: super.class.
biodb.TRACE[2025-09-06 16:03:01.136][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-09-06 16:03:01.137][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.138][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.139][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2025-09-06 16:03:01.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-09-06 16:03:01.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.143][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:03:01.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:03:01.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.147][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:03:01.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:03:01.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.151][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:03:01.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:03:01.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.184][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-09-06 16:03:01.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-09-06 16:03:01.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.191][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-09-06 16:03:01.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-09-06 16:03:01.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.195][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-09-06 16:03:01.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-09-06 16:03:01.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.199][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-06 16:03:01.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-06 16:03:01.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.203][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-06 16:03:01.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-06 16:03:01.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.207][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-06 16:03:01.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-06 16:03:01.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.211][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-06 16:03:01.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-06 16:03:01.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.215][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-06 16:03:01.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-06 16:03:01.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.219][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-06 16:03:01.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-06 16:03:01.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.223][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-09-06 16:03:01.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-09-06 16:03:01.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.226][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-09-06 16:03:01.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-09-06 16:03:01.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.230][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-09-06 16:03:01.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-09-06 16:03:01.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.234][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:03:01.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:03:01.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.238][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:03:01.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:03:01.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.241][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:03:01.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:03:01.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.245][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:03:01.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:03:01.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.249][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:03:01.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:03:01.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.253][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:03:01.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:03:01.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.256][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-09-06 16:03:01.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-09-06 16:03:01.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.260][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-09-06 16:03:01.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-09-06 16:03:01.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.264][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-09-06 16:03:01.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-09-06 16:03:01.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.268][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-09-06 16:03:01.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-09-06 16:03:01.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.271][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-09-06 16:03:01.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-09-06 16:03:01.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.275][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-09-06 16:03:01.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-09-06 16:03:01.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.279][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-06 16:03:01.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-06 16:03:01.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.283][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-06 16:03:01.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-06 16:03:01.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.286][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-06 16:03:01.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-06 16:03:01.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.290][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-06 16:03:01.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-06 16:03:01.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.294][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-06 16:03:01.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-06 16:03:01.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.298][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-06 16:03:01.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-06 16:03:01.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.301][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-06 16:03:01.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-06 16:03:01.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.305][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-06 16:03:01.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-06 16:03:01.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.309][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-06 16:03:01.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-06 16:03:01.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.313][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-06 16:03:01.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-06 16:03:01.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.316][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-06 16:03:01.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-06 16:03:01.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.320][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-06 16:03:01.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-06 16:03:01.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.324][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:03:01.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:03:01.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.327][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:03:01.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:03:01.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.334][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:03:01.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:03:01.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.338][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:03:01.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:03:01.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.342][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:03:01.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:03:01.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.346][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:03:01.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:03:01.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.349][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:03:01.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:03:01.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.353][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:03:01.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:03:01.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.357][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:03:01.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:03:01.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.361][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-06 16:03:01.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-06 16:03:01.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.364][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-06 16:03:01.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-06 16:03:01.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.368][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-06 16:03:01.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-06 16:03:01.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.372][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-09-06 16:03:01.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-06 16:03:01.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.376][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-09-06 16:03:01.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-06 16:03:01.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.379][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-09-06 16:03:01.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-06 16:03:01.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.383][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-09-06 16:03:01.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-06 16:03:01.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.387][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-06 16:03:01.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-06 16:03:01.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.391][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-06 16:03:01.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-06 16:03:01.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.394][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-06 16:03:01.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-06 16:03:01.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.398][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-09-06 16:03:01.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-06 16:03:01.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.418][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:03:01.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:03:01.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.422][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:03:01.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:03:01.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.425][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:03:01.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:03:01.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.429][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:03:01.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:03:01.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.433][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:03:01.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:03:01.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.437][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-09-06 16:03:01.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-09-06 16:03:01.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.440][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-09-06 16:03:01.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-09-06 16:03:01.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.444][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:03:01.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:03:01.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.448][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-09-06 16:03:01.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-09-06 16:03:01.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.452][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:03:01.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:03:01.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.455][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:03:01.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:03:01.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.459][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:03:01.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:03:01.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.463][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:03:01.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:03:01.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.470][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:03:01.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:03:01.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.474][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:03:01.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:03:01.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-09-06 16:03:01.477][biodb$getFactory()$createEntryFromCo ...] Accession numbers: HMDB0000001.
biodb.TRACE[2025-09-06 16:03:01.480][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-09-06 16:03:01.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-09-06 16:03:01.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.483][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-09-06 16:03:01.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-09-06 16:03:01.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.487][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-09-06 16:03:01.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-09-06 16:03:01.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.491][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-09-06 16:03:01.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-09-06 16:03:01.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.508][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:03:01.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:03:01.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.522][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-09-06 16:03:01.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-09-06 16:03:01.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.529][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:03:01.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:03:01.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.533][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:03:01.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:03:01.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.537][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:03:01.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:03:01.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.542][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:03:01.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:03:01.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.545][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:03:01.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:03:01.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.549][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:03:01.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:03:01.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.553][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-09-06 16:03:01.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-09-06 16:03:01.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.557][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-09-06 16:03:01.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-09-06 16:03:01.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.560][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-09-06 16:03:01.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-09-06 16:03:01.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.570][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:03:01.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:03:01.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.573][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:03:01.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:03:01.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.577][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:03:01.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:03:01.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.581][ef$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:03:01.582][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:03:01.583][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.584][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.585][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:03:01.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:03:01.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.595][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-06 16:03:01.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-06 16:03:01.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.598][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-06 16:03:01.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-06 16:03:01.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.602][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-06 16:03:01.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-06 16:03:01.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.610][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-06 16:03:01.611][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-06 16:03:01.612][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.612][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.613][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-06 16:03:01.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-06 16:03:01.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.623][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-09-06 16:03:01.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-09-06 16:03:01.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.627][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-09-06 16:03:01.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-09-06 16:03:01.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.631][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-09-06 16:03:01.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-09-06 16:03:01.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.634][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-09-06 16:03:01.635][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-09-06 16:03:01.636][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.637][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.638][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-09-06 16:03:01.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-09-06 16:03:01.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.648][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:03:01.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:03:01.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.652][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:03:01.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:03:01.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.655][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:03:01.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:03:01.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.659][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:03:01.660][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:03:01.661][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.662][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.663][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:03:01.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:03:01.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.673][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-06 16:03:01.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-06 16:03:01.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.676][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-06 16:03:01.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-06 16:03:01.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.680][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-06 16:03:01.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-06 16:03:01.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.684][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-06 16:03:01.685][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-06 16:03:01.686][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.686][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.687][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-06 16:03:01.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-06 16:03:01.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.697][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-06 16:03:01.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-06 16:03:01.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.701][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-06 16:03:01.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-06 16:03:01.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.705][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-06 16:03:01.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-06 16:03:01.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.708][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-06 16:03:01.709][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-06 16:03:01.710][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.711][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.712][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-06 16:03:01.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-06 16:03:01.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.722][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:03:01.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:03:01.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.725][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:03:01.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:03:01.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.729][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:03:01.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:03:01.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.733][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:03:01.734][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:03:01.735][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.736][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.740][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:03:01.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:03:01.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.749][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-09-06 16:03:01.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-09-06 16:03:01.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.753][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-09-06 16:03:01.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-09-06 16:03:01.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.757][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-09-06 16:03:01.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-09-06 16:03:01.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.761][ef$get] Asked field names are: description.
biodb.TRACE[2025-09-06 16:03:01.762][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-09-06 16:03:01.763][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.763][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.764][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-09-06 16:03:01.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-09-06 16:03:01.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.774][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-06 16:03:01.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-06 16:03:01.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.778][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-06 16:03:01.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-06 16:03:01.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.782][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-06 16:03:01.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-06 16:03:01.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.785][ef$get] Asked field names are: formula.
biodb.TRACE[2025-09-06 16:03:01.786][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-06 16:03:01.787][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.788][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.789][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-09-06 16:03:01.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-06 16:03:01.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.799][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-09-06 16:03:01.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-09-06 16:03:01.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.803][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-09-06 16:03:01.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-09-06 16:03:01.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.806][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-09-06 16:03:01.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-09-06 16:03:01.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.810][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-09-06 16:03:01.811][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-09-06 16:03:01.812][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.813][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.814][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-09-06 16:03:01.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-09-06 16:03:01.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.823][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:03:01.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:03:01.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.827][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:03:01.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:03:01.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.831][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:03:01.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:03:01.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.835][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:03:01.836][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:03:01.836][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.837][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.838][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:03:01.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:03:01.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.848][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-09-06 16:03:01.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-09-06 16:03:01.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.852][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-09-06 16:03:01.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-09-06 16:03:01.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.855][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-09-06 16:03:01.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-09-06 16:03:01.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.859][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-09-06 16:03:01.860][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-09-06 16:03:01.861][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.862][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.863][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-09-06 16:03:01.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-09-06 16:03:01.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.876][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:03:01.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:03:01.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.880][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:03:01.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:03:01.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.883][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:03:01.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:03:01.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.887][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:03:01.888][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:03:01.889][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.890][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.891][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:03:01.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:03:01.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.900][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:03:01.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:03:01.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.904][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:03:01.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:03:01.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.908][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:03:01.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:03:01.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.912][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:03:01.913][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:03:01.914][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.915][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.915][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:03:01.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:03:01.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.925][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-09-06 16:03:01.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-06 16:03:01.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.929][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-09-06 16:03:01.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-06 16:03:01.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.933][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-09-06 16:03:01.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-06 16:03:01.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.936][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-09-06 16:03:01.937][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-06 16:03:01.938][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.939][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.940][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-09-06 16:03:01.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-06 16:03:01.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.950][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-06 16:03:01.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-06 16:03:01.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.953][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-06 16:03:01.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-06 16:03:01.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.957][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-06 16:03:01.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-06 16:03:01.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.961][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-09-06 16:03:01.962][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-06 16:03:01.963][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.964][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.965][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-09-06 16:03:01.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-06 16:03:01.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.974][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-06 16:03:01.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-06 16:03:01.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.978][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-06 16:03:01.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-06 16:03:01.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.982][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-06 16:03:01.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-06 16:03:01.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.985][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-06 16:03:01.986][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-06 16:03:01.987][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.988][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.989][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-06 16:03:01.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-06 16:03:01.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:01.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:01.999][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-06 16:03:02.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-06 16:03:02.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:02.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:02.006][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-06 16:03:02.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-06 16:03:02.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:02.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:02.009][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-06 16:03:02.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-06 16:03:02.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:02.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:02.013][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-06 16:03:02.014][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-06 16:03:02.015][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:02.016][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:02.017][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-06 16:03:02.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-06 16:03:02.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:02.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:02.027][ef$get] Asked field names are: accession.
biodb.TRACE[2025-09-06 16:03:02.028][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-09-06 16:03:02.029][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:02.029][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:02.033][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-09-06 16:03:02.034][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-09-06 16:03:02.035][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:02.036][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:02.040][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-09-06 16:03:02.041][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-09-06 16:03:02.042][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:02.042][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:02.046][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-09-06 16:03:02.047][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-09-06 16:03:02.048][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:02.049][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:02.053][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-09-06 16:03:02.054][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-09-06 16:03:02.055][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:02.055][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:02.059][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:03:02.060][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-09-06 16:03:02.061][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:02.062][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:02.066][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:03:02.067][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-09-06 16:03:02.068][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:02.068][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:02.072][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-09-06 16:03:02.073][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-09-06 16:03:02.074][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:02.075][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:02.079][ef$get] Asked field names are: description.
biodb.TRACE[2025-09-06 16:03:02.080][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-09-06 16:03:02.081][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:02.081][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:02.085][ef$get] Asked field names are: formula.
biodb.TRACE[2025-09-06 16:03:02.086][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-09-06 16:03:02.087][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:02.088][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:02.092][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-09-06 16:03:02.093][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-09-06 16:03:02.093][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:02.094][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:02.098][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-09-06 16:03:02.099][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-09-06 16:03:02.100][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:02.101][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:02.105][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-09-06 16:03:02.106][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-09-06 16:03:02.106][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:02.107][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:02.111][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:03:02.112][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-09-06 16:03:02.113][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:02.114][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:02.118][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:03:02.119][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:03:02.119][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:02.120][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:02.124][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:03:02.125][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-09-06 16:03:02.126][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:02.127][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:02.134][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-06 16:03:02.135][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-06 16:03:02.136][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:02.137][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:02.140][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-09-06 16:03:02.141][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-09-06 16:03:02.142][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:02.143][ef$get] fields variable is a list.
biodb.INFO [2025-09-06 16:03:02.149][biodb::testThat]
biodb.INFO [2025-09-06 16:03:02.150][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-09-06 16:03:02.151][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-06 16:03:02.152][biodb::testThat]
biodb.DEBUG[2025-09-06 16:03:02.165][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-09-06 16:03:02.171][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.INFO [2025-09-06 16:03:02.175][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34" for "hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34".
biodb.DEBUG[2025-09-06 16:03:02.176][self$isDownloaded] Database hmdb.metabolites has not yet been downloaded.
biodb.INFO [2025-09-06 16:03:02.177][self$download] Downloading whole database of hmdb.metabolites.
biodb.INFO [2025-09-06 16:03:02.178][private$doDownload] Downloading HMDB metabolite database at "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip" ...
biodb.DEBUG[2025-09-06 16:03:02.180][sched$downloadFile] Downloading file "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
trying URL 'http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip'
biodb.INFO [2025-09-06 16:03:02.534][biodb::testThat]
biodb.INFO [2025-09-06 16:03:02.535][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-09-06 16:03:02.537][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-06 16:03:02.538][biodb::testThat]
biodb.TRACE[2025-09-06 16:03:02.541][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:03:02.542][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:03:02.543][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:02.544][ef$get] fields variable is a list.
biodb.DEBUG[2025-09-06 16:03:02.545][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "name".
biodb.DEBUG[2025-09-06 16:03:02.564][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-09-06 16:03:02.611][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-09-06 16:03:02.613][self$isDownloaded] Database hmdb.metabolites has not yet been downloaded.
biodb.INFO [2025-09-06 16:03:02.614][self$download] Downloading whole database of hmdb.metabolites.
biodb.INFO [2025-09-06 16:03:02.615][private$doDownload] Downloading HMDB metabolite database at "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip" ...
biodb.DEBUG[2025-09-06 16:03:02.629][sched$downloadFile] Downloading file "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
trying URL 'http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip'
biodb.INFO [2025-09-06 16:03:02.761][biodb::testThat]
biodb.INFO [2025-09-06 16:03:02.762][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-09-06 16:03:02.763][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-06 16:03:02.764][biodb::testThat]
biodb.DEBUG[2025-09-06 16:03:02.770][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-09-06 16:03:02.771][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-09-06 16:03:02.772][self$isDownloaded] Database hmdb.metabolites has not yet been downloaded.
biodb.INFO [2025-09-06 16:03:02.773][self$download] Downloading whole database of hmdb.metabolites.
biodb.INFO [2025-09-06 16:03:02.774][private$doDownload] Downloading HMDB metabolite database at "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip" ...
biodb.DEBUG[2025-09-06 16:03:02.776][sched$downloadFile] Downloading file "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
trying URL 'http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip'
biodb.INFO [2025-09-06 16:03:02.916][biodb::testThat]
biodb.INFO [2025-09-06 16:03:02.917][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-09-06 16:03:02.918][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-06 16:03:02.919][biodb::testThat]
biodb.DEBUG[2025-09-06 16:03:02.923][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-09-06 16:03:02.924][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-09-06 16:03:02.925][self$isDownloaded] Database hmdb.metabolites has not yet been downloaded.
biodb.INFO [2025-09-06 16:03:02.926][self$download] Downloading whole database of hmdb.metabolites.
biodb.INFO [2025-09-06 16:03:02.927][private$doDownload] Downloading HMDB metabolite database at "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip" ...
biodb.DEBUG[2025-09-06 16:03:02.929][rule$waitAsNeeded] Wait 0.250574 second(s).
biodb.DEBUG[2025-09-06 16:03:03.181][sched$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'
biodb.INFO [2025-09-06 16:03:03.343][biodb::testThat]
biodb.INFO [2025-09-06 16:03:03.344][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-09-06 16:03:03.345][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-06 16:03:03.346][biodb::testThat]
biodb.INFO [2025-09-06 16:03:03.354][biodb::testThat]
biodb.INFO [2025-09-06 16:03:03.355][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-09-06 16:03:03.356][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-06 16:03:03.357][biodb::testThat]
biodb.INFO [2025-09-06 16:03:03.363][biodb::testThat]
biodb.INFO [2025-09-06 16:03:03.364][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-09-06 16:03:03.365][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-06 16:03:03.366][biodb::testThat]
biodb.DEBUG[2025-09-06 16:03:03.369][function(conn, opt)] Trying to download "http://www.hmdb.ca/metabolites/HMDB0000001".
biodb.DEBUG[2025-09-06 16:03:03.584][getUrlContent] Use base::url() for downloading content of URL http://www.hmdb.ca/metabolites/HMDB0000001.
biodb.INFO [2025-09-06 16:03:03.998][biodb::testThat]
biodb.INFO [2025-09-06 16:03:03.999][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-09-06 16:03:04.000][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-09-06 16:03:04.001][biodb::testThat]
biodb.DEBUG[2025-09-06 16:03:04.081][getUrlContent] Use base::url() for downloading content of URL http://www.hmdb.ca/structures/HMDB0000001/image.png.
biodb.TRACE[2025-09-06 16:03:04.336][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:03:04.338][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:03:04.339][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:04.341][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:04.342][ef$get] Asked field names are: description.
biodb.TRACE[2025-09-06 16:03:04.343][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-09-06 16:03:04.344][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:04.345][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:04.346][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-06 16:03:04.348][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-06 16:03:04.349][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:04.350][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:04.351][ef$get] Asked field names are: name.
biodb.TRACE[2025-09-06 16:03:04.352][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-09-06 16:03:04.353][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:04.354][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:04.355][ef$get] Asked field names are: description.
biodb.TRACE[2025-09-06 16:03:04.356][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-09-06 16:03:04.357][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:04.358][ef$get] fields variable is a list.
biodb.TRACE[2025-09-06 16:03:04.359][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-09-06 16:03:04.360][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-09-06 16:03:04.361][ef$get] 1 fields were returned.
biodb.TRACE[2025-09-06 16:03:04.362][ef$get] fields variable is a list.
biodb.INFO [2025-09-06 16:03:04.363][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-09-06 16:03:04.504][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler
biodb.INFO [2025-09-06 16:03:04.506][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2025-09-06 16:03:04.507][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-09-06 16:03:04.508][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-09-06 16:03:04.509][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-09-06 16:03:04.510][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-09-06 16:03:04.510][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-09-06 16:03:04.511][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-09-06 16:03:04.512][FUN] Functions in observer 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 7 | WARN 8 | SKIP 0 | PASS 110 ]

══ 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)`: cannot open URL 'http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip'
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$downloadFile(url = zip.url, dest.file = tmpFile)
 9.               └─utils::download.file(...)
── Error ('test_long_100_generic.R:42:1'): We can search for an entry by searchable field ──
Error in `utils::download.file(url = url, destfile = dest.file, mode = "wb", 
    method = "auto", cacheOK = FALSE, quiet = FALSE)`: cannot open URL 'http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
  3.   └─conn$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)`: cannot open URL 'http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip'
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$downloadFile(url = zip.url, dest.file = tmpFile)
 10.                 └─utils::download.file(...)
── Error ('test_long_100_generic.R:42:1'): We can load an entry from the database. ──
Error in `utils::download.file(url = url, destfile = dest.file, mode = "wb", 
    method = "auto", cacheOK = FALSE, quiet = FALSE)`: cannot open URL 'http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
  3.   └─opt$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(...)
── Failure ('test_long_100_generic.R:42:1'): The entry page URL can be downloaded. ──
!is.na(content) is not TRUE

`actual`:       
`expected`: TRUE
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
 3.   └─testthat::expect_true(!is.na(content))
── Failure ('test_long_100_generic.R:42:1'): The entry page URL can be downloaded. ──
nchar(content) > 0 is not TRUE

`actual`:       
`expected`: TRUE
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
 3.   └─testthat::expect_true(nchar(content) > 0)
── Error ('test_long_100_generic.R:42:1'): The entry image URL can be downloaded. ──
Error in `charToRaw(content)`: argument must be a character vector of length 1
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
 3.   └─biodb:::getUrlContent(url, binary = TRUE)
 4.     └─biodb:::getBaseUrlContent(u, binary = binary)
 5.       └─base::charToRaw(content)

[ FAIL 7 | WARN 8 | SKIP 0 | PASS 110 ]
Error: Test failures
Execution halted

'R CMD check' output

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


* using log directory ‘/home/biocbuild/bbs-3.21-bioc-longtests/meat/biodbHmdb.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘biodbHmdb/DESCRIPTION’ ... OK
* this is package ‘biodbHmdb’ version ‘1.14.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbHmdb’ can be installed ... WARNING
Found the following significant warnings:
  EntryMaker.hpp:23:21: warning: ‘EntryMaker::accession_tag’ will be initialized after [-Wreorder]
  EntryMaker.hpp:22:14: warning:   ‘bool EntryMaker::closed’ [-Wreorder]
  EntryMaker.cpp:5:1: warning:   when initialized here [-Wreorder]
See ‘/home/biocbuild/bbs-3.21-bioc-longtests/meat/biodbHmdb.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... 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:
   2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
   3.   └─testthat::expect_true(nchar(content) > 0)
  ── Error ('test_long_100_generic.R:42:1'): The entry image URL can be downloaded. ──
  Error in `charToRaw(content)`: argument must be a character vector of length 1
  Backtrace:
      ▆
   1. ├─base::do.call(fct, params)
   2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
   3.   └─biodb:::getUrlContent(url, binary = TRUE)
   4.     └─biodb:::getBaseUrlContent(u, binary = binary)
   5.       └─base::charToRaw(content)
  
  [ FAIL 7 | WARN 8 | SKIP 0 | PASS 110 ]
  Error: Test failures
  Execution halted
* DONE

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

Installation output

biodbHmdb.Rcheck/00install.out

* installing *source* package ‘biodbHmdb’ ...
** this is package ‘biodbHmdb’ version ‘1.14.0’
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c EntryMaker.cpp -o EntryMaker.o
In file included from EntryMaker.cpp:1:
EntryMaker.hpp: In constructor ‘EntryMaker::EntryMaker()’:
EntryMaker.hpp:23:21: warning: ‘EntryMaker::accession_tag’ will be initialized after [-Wreorder]
   23 |         TagDetector accession_tag;
      |                     ^~~~~~~~~~~~~
EntryMaker.hpp:22:14: warning:   ‘bool EntryMaker::closed’ [-Wreorder]
   22 |         bool closed;
      |              ^~~~~~
EntryMaker.cpp:5:1: warning:   when initialized here [-Wreorder]
    5 | EntryMaker::EntryMaker() :
      | ^~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c FileEntryMaker.cpp -o FileEntryMaker.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c StringEnrtryMaker.cpp -o StringEnrtryMaker.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c TagDetector.cpp -o TagDetector.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c XmlSplitter.cpp -o XmlSplitter.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c extractXmlEntries.cpp -o extractXmlEntries.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c test-100-TagDetector.cpp -o test-100-TagDetector.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c test-150-StringEntryMaker.cpp -o test-150-StringEntryMaker.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c test-200-XmlSplitter.cpp -o test-200-XmlSplitter.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c test-runner.cpp -o test-runner.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.21-bioc/R/lib -L/usr/local/lib -o biodbHmdb.so EntryMaker.o FileEntryMaker.o RcppExports.o StringEnrtryMaker.o TagDetector.o XmlSplitter.o extractXmlEntries.o test-100-TagDetector.o test-150-StringEntryMaker.o test-200-XmlSplitter.o test-runner.o -L/home/biocbuild/bbs-3.21-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.21-bioc-longtests/meat/biodbHmdb.Rcheck/00LOCK-biodbHmdb/00new/biodbHmdb/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
No man pages found in package  ‘biodbHmdb’ 
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (biodbHmdb)