Back to Long Tests report for BioC 3.21

This page was generated on 2025-01-25 23:55 -0500 (Sat, 25 Jan 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" 4658
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" 4455
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences" 4463
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 7/30HostnameOS / ArchCHECK
biodbHmdb 1.13.0  (landing page)
Pierrick Roger
Snapshot Date: 2025-01-25 09:55 -0500 (Sat, 25 Jan 2025)
git_url: https://git.bioconductor.org/packages/biodbHmdb
git_branch: devel
git_last_commit: d2b9830
git_last_commit_date: 2024-10-29 11:06:39 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  ERROR  
palomino7Windows Server 2022 Datacenter / x64  ERROR  
lconwaymacOS 12.7.1 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: 1.13.0
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_1.13.0.tar.gz
StartedAt: 2025-01-25 16:04:14 -0500 (Sat, 25 Jan 2025)
EndedAt: 2025-01-25 16:11:39 -0500 (Sat, 25 Jan 2025)
EllapsedTime: 444.3 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbHmdb.Rcheck
Warnings: NA

Tests output

biodbHmdb.Rcheck/tests/testthat.Rout.fail


R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"
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Platform: x86_64-pc-linux-gnu

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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbHmdb)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbHmdb")
biodb.INFO [2025-01-25 16:05:16.781][biodb::testContext]
biodb.INFO [2025-01-25 16:05:16.783][biodb::testContext] ********************************************************************************
biodb.INFO [2025-01-25 16:05:16.784][biodb::testContext] Test context - Generic long tests
biodb.INFO [2025-01-25 16:05:16.785][biodb::testContext] ********************************************************************************
biodb.INFO [2025-01-25 16:05:16.786][biodb::testContext]
biodb.INFO [2025-01-25 16:05:16.791][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2025-01-25 16:05:16.793][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-01-25 16:05:16.800][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-25 16:05:16.801][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-01-25 16:05:16.802][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-01-25 16:05:16.802][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:16.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:16.804][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:16.805][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-01-25 16:05:16.822][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-01-25 16:05:16.823][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:16.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:16.825][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:16.825][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-01-25 16:05:16.826][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-01-25 16:05:16.827][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:16.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:16.829][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:16.830][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-01-25 16:05:16.831][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-01-25 16:05:16.832][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-01-25 16:05:16.833][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:16.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:16.834][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:16.835][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-01-25 16:05:16.836][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-01-25 16:05:16.837][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-01-25 16:05:16.838][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:16.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:16.839][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:16.840][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-01-25 16:05:16.841][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-01-25 16:05:16.842][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:16.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:16.844][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:16.845][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-01-25 16:05:16.846][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-01-25 16:05:16.847][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-01-25 16:05:16.847][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:16.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:16.849][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:16.850][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-01-25 16:05:16.851][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-01-25 16:05:16.852][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:16.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:16.853][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:16.854][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-01-25 16:05:16.855][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-01-25 16:05:16.856][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-01-25 16:05:16.857][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:16.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:16.859][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:16.859][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-01-25 16:05:16.860][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-01-25 16:05:16.861][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-01-25 16:05:16.862][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-01-25 16:05:16.863][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-01-25 16:05:16.864][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-01-25 16:05:16.865][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:16.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:16.867][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:16.868][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-01-25 16:05:16.869][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-01-25 16:05:16.869][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:16.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:16.871][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:16.872][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-01-25 16:05:16.873][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-01-25 16:05:16.874][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:16.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:16.875][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:16.876][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-01-25 16:05:16.877][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-01-25 16:05:16.878][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:16.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:16.880][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:16.881][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-01-25 16:05:16.882][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-01-25 16:05:16.882][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:16.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:16.884][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:16.885][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-01-25 16:05:16.886][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-01-25 16:05:16.887][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:16.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:16.889][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:16.889][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-01-25 16:05:16.890][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-01-25 16:05:16.894][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-01-25 16:05:16.895][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:16.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:16.897][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:16.897][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-01-25 16:05:16.898][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-01-25 16:05:16.899][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-01-25 16:05:16.900][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:16.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:16.902][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:16.905][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-01-25 16:05:16.936][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-25 16:05:16.956][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-01-25 16:05:16.957][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-25 16:05:16.958][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-25 16:05:16.959][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-25 16:05:16.960][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-25 16:05:16.961][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-25 16:05:16.962][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-25 16:05:16.963][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-01-25 16:05:16.964][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-25 16:05:16.964][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-25 16:05:16.965][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-01-25 16:05:16.966][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-25 16:05:16.967][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:05:16.968][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-25 16:05:16.969][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-25 16:05:16.969][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-01-25 16:05:16.969][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-01-25 16:05:16.969][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-01-25 16:05:16.969][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-01-25 16:05:16.970][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-25 16:05:16.971][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-25 16:05:16.972][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-25 16:05:16.973][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-25 16:05:16.974][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-25 16:05:16.974][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-25 16:05:16.975][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-25 16:05:16.976][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:05:16.977][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-25 16:05:16.978][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-25 16:05:16.979][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-25 16:05:16.980][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:05:16.981][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-01-25 16:05:16.983][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-25 16:05:16.984][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-01-25 16:05:16.985][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-25 16:05:16.985][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-25 16:05:16.986][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-25 16:05:16.987][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-25 16:05:16.988][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-25 16:05:16.989][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-25 16:05:16.990][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-01-25 16:05:16.991][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-25 16:05:16.992][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-25 16:05:16.993][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-01-25 16:05:16.994][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-25 16:05:16.995][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:05:16.996][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-25 16:05:16.997][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-25 16:05:16.997][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-01-25 16:05:16.997][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-01-25 16:05:16.997][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-01-25 16:05:16.997][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-01-25 16:05:16.998][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-25 16:05:16.999][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-25 16:05:16.999][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-25 16:05:17.000][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-25 16:05:17.001][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-25 16:05:17.002][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-25 16:05:17.003][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-25 16:05:17.004][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:05:17.005][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-25 16:05:17.006][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-25 16:05:17.006][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-25 16:05:17.007][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:05:17.008][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-01-25 16:05:17.010][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-01-25 16:05:17.011][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-01-25 16:05:17.012][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-25 16:05:17.013][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-25 16:05:17.014][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-25 16:05:17.015][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-25 16:05:17.016][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-25 16:05:17.017][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-25 16:05:17.018][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-01-25 16:05:17.018][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-25 16:05:17.019][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-01-25 16:05:17.020][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-01-25 16:05:17.021][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-25 16:05:17.022][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:05:17.023][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-25 16:05:17.024][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:05:17.025][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-25 16:05:17.026][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-25 16:05:17.027][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-25 16:05:17.028][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-25 16:05:17.029][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-25 16:05:17.029][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-25 16:05:17.030][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-25 16:05:17.031][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:05:17.032][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-25 16:05:17.033][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-25 16:05:17.034][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-25 16:05:17.035][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:05:17.036][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-01-25 16:05:17.037][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-01-25 16:05:17.038][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-01-25 16:05:17.039][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-25 16:05:17.040][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-25 16:05:17.041][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-25 16:05:17.042][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-25 16:05:17.043][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-25 16:05:17.044][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-25 16:05:17.045][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-01-25 16:05:17.046][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-25 16:05:17.047][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-01-25 16:05:17.048][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-01-25 16:05:17.049][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-25 16:05:17.050][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:05:17.050][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-25 16:05:17.051][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:05:17.052][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-25 16:05:17.053][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-25 16:05:17.054][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-25 16:05:17.055][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-25 16:05:17.056][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-25 16:05:17.057][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-25 16:05:17.058][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-25 16:05:17.059][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:05:17.059][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-25 16:05:17.060][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-25 16:05:17.061][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-25 16:05:17.062][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:05:17.066][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-25 16:05:17.066][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:17.067][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:17.068][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:17.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:17.070][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:17.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:17.071][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:17.072][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:17.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:17.074][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:17.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:17.076][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:17.077][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:17.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:17.078][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:17.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:17.080][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:17.081][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:17.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:17.082][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:17.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:17.084][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:17.085][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:17.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:17.086][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:17.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:17.088][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:17.089][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:17.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:17.091][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:17.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:17.092][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:17.093][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:17.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:17.095][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:17.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:17.096][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:17.097][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:17.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:17.099][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:17.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:17.101][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:17.102][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:17.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:17.103][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:17.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:17.105][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:17.106][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:17.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:17.107][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:17.108][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:17.109][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:17.110][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:17.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:17.115][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:17.116][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:17.117][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:17.118][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:17.119][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:17.119][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:17.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:17.121][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:17.122][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:17.123][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:17.123][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:17.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:17.125][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:17.126][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:17.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:17.128][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:17.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:17.129][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:17.130][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:17.131][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:17.132][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:17.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:17.133][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:17.134][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:17.135][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:17.136][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:17.137][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:17.137][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:17.138][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:17.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:17.140][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:17.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:17.142][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:17.149][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-01-25 16:05:17.156][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-01-25 16:05:17.157][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-01-25 16:05:17.159][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-01-25 16:05:17.160][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-01-25 16:05:17.162][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-01-25 16:05:17.163][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-01-25 16:05:17.164][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-01-25 16:05:17.166][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-01-25 16:05:17.167][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-01-25 16:05:17.169][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-01-25 16:05:17.170][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-01-25 16:05:17.172][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-01-25 16:05:17.173][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-01-25 16:05:17.175][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-01-25 16:05:17.176][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-01-25 16:05:17.178][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-01-25 16:05:17.179][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-01-25 16:05:17.180][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-01-25 16:05:17.182][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-01-25 16:05:17.183][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-01-25 16:05:17.185][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-01-25 16:05:17.186][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-01-25 16:05:17.188][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-01-25 16:05:17.189][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-01-25 16:05:17.191][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-01-25 16:05:17.192][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-01-25 16:05:17.194][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-01-25 16:05:17.195][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-01-25 16:05:17.197][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-01-25 16:05:17.198][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-01-25 16:05:17.200][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-01-25 16:05:17.201][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-01-25 16:05:17.203][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-01-25 16:05:17.204][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-01-25 16:05:17.206][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-01-25 16:05:17.207][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-01-25 16:05:17.209][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-01-25 16:05:17.210][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-01-25 16:05:17.211][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-01-25 16:05:17.213][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-01-25 16:05:17.214][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-01-25 16:05:17.216][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-01-25 16:05:17.217][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-01-25 16:05:17.219][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-01-25 16:05:17.220][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-01-25 16:05:17.222][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-01-25 16:05:17.223][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-01-25 16:05:17.225][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-01-25 16:05:17.226][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-01-25 16:05:17.228][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-01-25 16:05:17.229][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-01-25 16:05:17.230][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-01-25 16:05:17.232][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-01-25 16:05:17.233][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-01-25 16:05:17.235][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-01-25 16:05:17.236][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-01-25 16:05:17.238][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-01-25 16:05:17.239][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-01-25 16:05:17.241][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-01-25 16:05:17.242][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-01-25 16:05:17.244][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-01-25 16:05:17.245][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-01-25 16:05:17.247][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-01-25 16:05:17.248][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-01-25 16:05:17.250][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-01-25 16:05:17.251][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-01-25 16:05:17.252][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-01-25 16:05:17.254][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-01-25 16:05:17.255][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-01-25 16:05:17.257][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-01-25 16:05:17.258][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-01-25 16:05:17.260][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-01-25 16:05:17.261][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-01-25 16:05:17.263][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-01-25 16:05:17.264][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-01-25 16:05:17.265][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-01-25 16:05:17.267][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-01-25 16:05:17.268][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-01-25 16:05:17.270][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-01-25 16:05:17.271][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-01-25 16:05:17.273][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-01-25 16:05:17.274][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-01-25 16:05:17.281][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-01-25 16:05:17.283][initialize] This is biodb version 1.15.0.
biodb.DEBUG[2025-01-25 16:05:17.286][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-25 16:05:17.287][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:17.288][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:17.289][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:17.290][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:17.295][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:17.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:05:17.297][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:05:17.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:17.299][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:17.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:17.300][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:17.301][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:17.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:05:17.303][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:05:17.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:17.305][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:17.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:17.318][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:17.319][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:17.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:05:17.321][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:05:17.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:17.323][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:17.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:17.324][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:17.325][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:17.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:05:17.327][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:05:17.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:17.329][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:17.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:17.331][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:17.332][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:17.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:05:17.333][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:05:17.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:17.335][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:17.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:17.337][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:17.338][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:17.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:05:17.340][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:05:17.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:17.342][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:17.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:17.344][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:17.345][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:17.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:05:17.346][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:05:17.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:17.348][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:17.349][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:17.350][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:17.351][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:17.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:05:17.352][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:05:17.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:17.354][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:17.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:17.356][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:17.357][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:17.357][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:05:17.358][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:05:17.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:17.360][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:17.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:17.361][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:17.362][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:17.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:05:17.364][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:05:17.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:17.366][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:17.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:17.367][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:17.368][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:17.369][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:05:17.370][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:05:17.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:17.371][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:17.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:17.373][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:17.374][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:17.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:05:17.376][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:05:17.376][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:17.377][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:17.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:17.379][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:17.380][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:17.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:05:17.381][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:05:17.382][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:17.383][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:17.384][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:17.385][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:17.386][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:17.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:05:17.387][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:05:17.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:17.389][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:17.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:17.391][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:17.391][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:17.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:05:17.393][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:05:17.394][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:17.395][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:17.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:17.396][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:17.397][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:17.398][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:05:17.399][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:05:17.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:17.400][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:17.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:17.402][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:17.403][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:17.404][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:05:17.405][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:05:17.405][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:17.406][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:17.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:17.408][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:17.409][biodb$getConfig()$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-01-25 16:05:17.410][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:05:17.411][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:05:17.411][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:05:17.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:17.413][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:17.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:17.415][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:05:17.416][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.21-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/definitions.yml".
biodb.DEBUG[2025-01-25 16:05:17.426][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2025-01-25 16:05:17.427][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-25 16:05:17.428][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-01-25 16:05:17.429][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-25 16:05:17.430][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-25 16:05:17.431][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-01-25 16:05:17.432][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2025-01-25 16:05:17.433][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-01-25 16:05:17.434][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-25 16:05:17.435][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-01-25 16:05:17.436][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-25 16:05:17.437][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-25 16:05:17.438][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2025-01-25 16:05:17.439][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-25 16:05:17.440][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2025-01-25 16:05:17.440][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2025-01-25 16:05:17.440][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2025-01-25 16:05:17.440][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2025-01-25 16:05:17.440][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2025-01-25 16:05:17.440][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2025-01-25 16:05:17.440][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2025-01-25 16:05:17.440][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2025-01-25 16:05:17.440][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2025-01-25 16:05:17.440][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2025-01-25 16:05:17.440][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2025-01-25 16:05:17.440][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2025-01-25 16:05:17.440][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2025-01-25 16:05:17.440][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2025-01-25 16:05:17.440][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2025-01-25 16:05:17.440][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2025-01-25 16:05:17.440][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2025-01-25 16:05:17.440][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2025-01-25 16:05:17.441][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-01-25 16:05:17.442][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-25 16:05:17.442][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2025-01-25 16:05:17.442][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2025-01-25 16:05:17.443][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-01-25 16:05:17.444][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-25 16:05:17.445][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-25 16:05:17.446][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-25 16:05:17.447][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-25 16:05:17.447][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-25 16:05:17.448][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-25 16:05:17.449][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2025-01-25 16:05:17.449][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2025-01-25 16:05:17.450][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-25 16:05:17.451][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-25 16:05:17.452][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-01-25 16:05:17.453][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:05:17.459][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2025-01-25 16:05:17.460][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-01-25 16:05:17.461][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-01-25 16:05:17.463][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-01-25 16:05:17.464][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-01-25 16:05:17.486][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2025-01-25 16:05:17.487][initialize] Register connector hmdb.metabolites with the request scheduler
biodb.DEBUG[2025-01-25 16:05:17.491][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites.
biodb.DEBUG[2025-01-25 16:05:17.524][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2025-01-25 16:05:17.527][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-01-25 16:05:17.528][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-01-25 16:05:17.530][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca".
biodb.DEBUG[2025-01-25 16:05:17.531][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.INFO [2025-01-25 16:05:17.539][biodb::testThat]
biodb.INFO [2025-01-25 16:05:17.540][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-01-25 16:05:17.541][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-25 16:05:17.541][biodb::testThat]
biodb.TRACE[2025-01-25 16:05:17.545][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[2025-01-25 16:05:17.547][biodb$getFactory()$createEntryFromCo ...] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-01-25 16:05:17.550][biodb$getFactory()$createEntryFromCo ...] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-01-25 16:05:17.557][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-25 16:05:17.558][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:05:17.559][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:05:17.570][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:05:17.571][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:05:17.572][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:05:17.573][FUN] Functions in observer BiodbConfig: [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[2025-01-25 16:05:17.583][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:05:17.584][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:05:17.585][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:17.586][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:17.588][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:05:17.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:05:17.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:17.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:17.602][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-25 16:05:17.603][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-25 16:05:17.604][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:17.605][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:17.629][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-25 16:05:17.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-25 16:05:17.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:17.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:17.633][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-25 16:05:17.634][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-25 16:05:17.635][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:17.636][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:17.637][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-25 16:05:17.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-25 16:05:17.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:17.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:17.641][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-25 16:05:17.642][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-25 16:05:17.643][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:17.644][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:17.645][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-25 16:05:17.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-25 16:05:17.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:17.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:17.649][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-25 16:05:17.650][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-25 16:05:17.651][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:17.652][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:17.653][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-25 16:05:17.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-25 16:05:17.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:17.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:17.657][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-25 16:05:17.658][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-25 16:05:17.658][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:17.659][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:17.660][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-25 16:05:17.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-25 16:05:17.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:17.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:17.664][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-25 16:05:17.665][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-25 16:05:17.666][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:17.667][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:17.668][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-25 16:05:17.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-25 16:05:17.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:17.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:17.672][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-25 16:05:17.673][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-25 16:05:17.674][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:17.675][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:17.676][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-25 16:05:17.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-25 16:05:17.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:17.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:17.680][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-25 16:05:17.681][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-25 16:05:17.681][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:17.682][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:17.690][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-25 16:05:17.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-25 16:05:17.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:17.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:17.694][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-25 16:05:17.695][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-25 16:05:17.696][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:17.697][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:17.698][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-25 16:05:17.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-25 16:05:17.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:17.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:17.702][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-25 16:05:17.703][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-25 16:05:17.704][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:17.704][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:17.706][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-25 16:05:17.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-25 16:05:17.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:17.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:17.709][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-25 16:05:17.710][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-25 16:05:17.711][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:17.712][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:17.713][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-25 16:05:17.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-25 16:05:17.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:17.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:17.717][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-25 16:05:17.718][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:05:17.719][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:17.720][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:17.721][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-25 16:05:17.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:05:17.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:17.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:17.725][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-25 16:05:17.726][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-25 16:05:17.727][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:17.728][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:17.729][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-25 16:05:17.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-25 16:05:17.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:17.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:17.733][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:05:17.734][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:05:17.734][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:17.735][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:17.736][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:05:17.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:05:17.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:17.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:17.740][ef$get] Asked field names are: description.
biodb.TRACE[2025-01-25 16:05:17.741][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-01-25 16:05:17.742][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:17.743][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:17.744][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-25 16:05:17.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-25 16:05:17.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:17.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:17.748][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-25 16:05:17.749][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-25 16:05:17.750][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:17.751][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:17.752][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-25 16:05:17.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-25 16:05:17.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:17.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:17.756][ef$get] Asked field names are: super.class.
biodb.TRACE[2025-01-25 16:05:17.757][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-25 16:05:17.757][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:17.758][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:17.760][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2025-01-25 16:05:17.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-25 16:05:17.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:17.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:17.763][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:05:17.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:05:17.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:17.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:17.767][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:05:17.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:05:17.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:17.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:17.771][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:05:17.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:05:17.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:17.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:17.805][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-25 16:05:17.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-25 16:05:17.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:17.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:17.808][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-25 16:05:17.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-25 16:05:17.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:17.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:17.812][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-25 16:05:17.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-25 16:05:17.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:17.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:17.816][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-25 16:05:17.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-25 16:05:17.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:17.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:17.820][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-25 16:05:17.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-25 16:05:17.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:17.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:17.827][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-25 16:05:17.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-25 16:05:17.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:17.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:17.830][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-25 16:05:17.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-25 16:05:17.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:17.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:17.834][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-25 16:05:17.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-25 16:05:17.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:17.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:17.838][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-25 16:05:17.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-25 16:05:17.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:17.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:17.842][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-25 16:05:17.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-25 16:05:17.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:17.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:17.845][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-25 16:05:17.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-25 16:05:17.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:17.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:17.849][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-25 16:05:17.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-25 16:05:17.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:17.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:17.853][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-25 16:05:17.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-25 16:05:17.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:17.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:17.856][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-25 16:05:17.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-25 16:05:17.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:17.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:17.860][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-25 16:05:17.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-25 16:05:17.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:17.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:17.864][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-25 16:05:17.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-25 16:05:17.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:17.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:17.868][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-25 16:05:17.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-25 16:05:17.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:17.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:17.872][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-25 16:05:17.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-25 16:05:17.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:17.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:17.875][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-01-25 16:05:17.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-25 16:05:17.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:17.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:17.879][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-01-25 16:05:17.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-25 16:05:17.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:17.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:17.883][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-01-25 16:05:17.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-25 16:05:17.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:17.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:17.887][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-25 16:05:17.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-25 16:05:17.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:17.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:17.890][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-25 16:05:17.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-25 16:05:17.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:17.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:17.894][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-25 16:05:17.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-25 16:05:17.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:17.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:17.898][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-25 16:05:17.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-25 16:05:17.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:17.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:17.901][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-25 16:05:17.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-25 16:05:17.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:17.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:17.905][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-25 16:05:17.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-25 16:05:17.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:17.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:17.909][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-25 16:05:17.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-25 16:05:17.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:17.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:17.913][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-25 16:05:17.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-25 16:05:17.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:17.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:17.916][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-25 16:05:17.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-25 16:05:17.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:17.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:17.920][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-25 16:05:17.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:05:17.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:17.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:17.924][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-25 16:05:17.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:05:17.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:17.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:17.927][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-25 16:05:17.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:05:17.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:17.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:17.931][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-25 16:05:17.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-25 16:05:17.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:17.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:17.935][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-25 16:05:17.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-25 16:05:17.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:17.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:17.939][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-25 16:05:17.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-25 16:05:17.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:17.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:17.942][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-25 16:05:17.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-25 16:05:17.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:17.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:17.946][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-25 16:05:17.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-25 16:05:17.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:17.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:17.950][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-25 16:05:17.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-25 16:05:17.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:17.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:17.954][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:05:17.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:05:17.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:17.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:17.957][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:05:17.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:05:17.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:17.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:17.961][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:05:17.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:05:17.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:17.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:17.968][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-25 16:05:17.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-25 16:05:17.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:17.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:17.972][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-25 16:05:17.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-25 16:05:17.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:17.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:17.976][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-25 16:05:17.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-25 16:05:17.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:17.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:17.979][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-25 16:05:17.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-25 16:05:17.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:17.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:17.983][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-25 16:05:17.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-25 16:05:17.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:17.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:17.987][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-25 16:05:17.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-25 16:05:17.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:17.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:17.990][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-25 16:05:17.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-25 16:05:17.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:17.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:17.994][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-25 16:05:17.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-25 16:05:17.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:17.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:17.998][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-25 16:05:17.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-25 16:05:18.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.002][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-01-25 16:05:18.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:05:18.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.005][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-25 16:05:18.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:05:18.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.009][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-25 16:05:18.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:05:18.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.013][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-25 16:05:18.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:05:18.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.017][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-01-25 16:05:18.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:05:18.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.038][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:05:18.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:05:18.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.042][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:05:18.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:05:18.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.046][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:05:18.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:05:18.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.050][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:05:18.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:05:18.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.053][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:05:18.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:05:18.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.057][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-01-25 16:05:18.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-01-25 16:05:18.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.061][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-01-25 16:05:18.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-01-25 16:05:18.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.065][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:05:18.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:05:18.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.069][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-01-25 16:05:18.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-01-25 16:05:18.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.073][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:05:18.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:05:18.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.077][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:05:18.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:05:18.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.080][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:05:18.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:05:18.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.084][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:05:18.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:05:18.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.088][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:05:18.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:05:18.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.092][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:05:18.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:05:18.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-25 16:05:18.095][biodb$getFactory()$createEntryFromCo ...] Accession numbers: HMDB0000001.
biodb.TRACE[2025-01-25 16:05:18.098][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-25 16:05:18.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-25 16:05:18.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.102][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-25 16:05:18.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-25 16:05:18.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.109][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-01-25 16:05:18.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-01-25 16:05:18.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.113][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-01-25 16:05:18.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-01-25 16:05:18.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.130][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:05:18.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:05:18.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.146][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-01-25 16:05:18.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-01-25 16:05:18.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.154][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:05:18.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:05:18.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.158][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:05:18.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:05:18.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.161][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:05:18.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:05:18.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.167][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:05:18.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:05:18.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.171][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:05:18.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:05:18.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.174][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:05:18.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:05:18.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.178][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-01-25 16:05:18.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-01-25 16:05:18.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.182][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-01-25 16:05:18.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-01-25 16:05:18.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.186][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-01-25 16:05:18.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-01-25 16:05:18.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.196][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:05:18.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:05:18.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.199][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:05:18.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:05:18.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.203][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:05:18.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:05:18.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.207][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:05:18.208][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:05:18.209][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.210][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.211][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:05:18.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:05:18.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.221][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-25 16:05:18.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-25 16:05:18.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.225][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-25 16:05:18.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-25 16:05:18.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.229][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-25 16:05:18.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-25 16:05:18.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.233][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-25 16:05:18.234][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-25 16:05:18.234][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.235][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.236][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-25 16:05:18.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-25 16:05:18.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.247][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-25 16:05:18.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-25 16:05:18.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.255][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-25 16:05:18.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-25 16:05:18.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.258][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-25 16:05:18.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-25 16:05:18.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.262][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-25 16:05:18.263][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-25 16:05:18.264][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.265][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.266][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-25 16:05:18.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-25 16:05:18.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.276][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-25 16:05:18.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-25 16:05:18.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.280][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-25 16:05:18.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-25 16:05:18.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.284][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-25 16:05:18.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-25 16:05:18.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.287][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-25 16:05:18.288][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-25 16:05:18.289][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.290][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.291][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-25 16:05:18.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-25 16:05:18.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.301][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-25 16:05:18.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-25 16:05:18.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.305][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-25 16:05:18.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-25 16:05:18.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.309][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-25 16:05:18.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-25 16:05:18.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.313][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-25 16:05:18.314][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-25 16:05:18.314][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.315][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.316][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-25 16:05:18.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-25 16:05:18.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.327][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-25 16:05:18.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-25 16:05:18.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.331][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-25 16:05:18.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-25 16:05:18.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.334][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-25 16:05:18.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-25 16:05:18.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.338][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-25 16:05:18.339][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-25 16:05:18.340][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.341][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.342][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-25 16:05:18.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-25 16:05:18.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.353][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:05:18.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:05:18.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.356][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:05:18.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:05:18.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.360][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:05:18.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:05:18.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.364][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:05:18.365][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:05:18.366][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.367][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.368][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:05:18.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:05:18.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.378][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-25 16:05:18.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-25 16:05:18.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.381][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-25 16:05:18.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-25 16:05:18.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.385][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-25 16:05:18.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-25 16:05:18.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.389][ef$get] Asked field names are: description.
biodb.TRACE[2025-01-25 16:05:18.394][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-01-25 16:05:18.394][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.395][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.396][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-25 16:05:18.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-25 16:05:18.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.406][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-25 16:05:18.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-25 16:05:18.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.410][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-25 16:05:18.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-25 16:05:18.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.414][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-25 16:05:18.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-25 16:05:18.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.417][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-25 16:05:18.418][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-25 16:05:18.419][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.420][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.421][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-25 16:05:18.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-25 16:05:18.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.431][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-25 16:05:18.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-25 16:05:18.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.435][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-25 16:05:18.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-25 16:05:18.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.439][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-25 16:05:18.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-25 16:05:18.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.443][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-25 16:05:18.444][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-25 16:05:18.445][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.445][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.446][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-25 16:05:18.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-25 16:05:18.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.457][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-25 16:05:18.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-25 16:05:18.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.460][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-25 16:05:18.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-25 16:05:18.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.464][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-25 16:05:18.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-25 16:05:18.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.468][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-25 16:05:18.469][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-25 16:05:18.470][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.470][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.471][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-25 16:05:18.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-25 16:05:18.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.482][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-01-25 16:05:18.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-25 16:05:18.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.485][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-01-25 16:05:18.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-25 16:05:18.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.489][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-01-25 16:05:18.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-25 16:05:18.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.493][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-01-25 16:05:18.494][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-25 16:05:18.495][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.496][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.497][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-01-25 16:05:18.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-25 16:05:18.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.507][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-25 16:05:18.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-25 16:05:18.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.511][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-25 16:05:18.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-25 16:05:18.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.514][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-25 16:05:18.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-25 16:05:18.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.518][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-25 16:05:18.519][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-25 16:05:18.520][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.521][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.522][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-25 16:05:18.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-25 16:05:18.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.535][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-25 16:05:18.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-25 16:05:18.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.539][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-25 16:05:18.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-25 16:05:18.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.543][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-25 16:05:18.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-25 16:05:18.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.547][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-25 16:05:18.548][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-25 16:05:18.548][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.549][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.550][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-25 16:05:18.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-25 16:05:18.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.561][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-25 16:05:18.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-25 16:05:18.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.564][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-25 16:05:18.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-25 16:05:18.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.568][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-25 16:05:18.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-25 16:05:18.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.572][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-25 16:05:18.573][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-25 16:05:18.574][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.575][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.575][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-25 16:05:18.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-25 16:05:18.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.586][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-25 16:05:18.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-25 16:05:18.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.589][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-25 16:05:18.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-25 16:05:18.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.593][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-25 16:05:18.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-25 16:05:18.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.597][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-25 16:05:18.598][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-25 16:05:18.599][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.600][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.601][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-25 16:05:18.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-25 16:05:18.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.611][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-25 16:05:18.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:05:18.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.615][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-25 16:05:18.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:05:18.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.618][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-25 16:05:18.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:05:18.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.622][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-25 16:05:18.623][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:05:18.624][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.625][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.626][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-25 16:05:18.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:05:18.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.636][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-25 16:05:18.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-25 16:05:18.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.640][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-25 16:05:18.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-25 16:05:18.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.643][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-25 16:05:18.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-25 16:05:18.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.647][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-25 16:05:18.648][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-25 16:05:18.649][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.650][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.651][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-25 16:05:18.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-25 16:05:18.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.661][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:05:18.662][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:05:18.663][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.664][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.672][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-25 16:05:18.673][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-25 16:05:18.673][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.674][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.678][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-25 16:05:18.679][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-25 16:05:18.680][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.681][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.685][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-25 16:05:18.686][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-25 16:05:18.687][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.688][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.691][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-25 16:05:18.692][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-25 16:05:18.693][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.694][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.698][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-25 16:05:18.699][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-25 16:05:18.700][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.701][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.705][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-25 16:05:18.706][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-25 16:05:18.706][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.707][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.711][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-01-25 16:05:18.712][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-25 16:05:18.713][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.714][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.718][ef$get] Asked field names are: description.
biodb.TRACE[2025-01-25 16:05:18.719][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-01-25 16:05:18.720][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.721][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.724][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-25 16:05:18.725][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-25 16:05:18.726][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.727][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.731][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-25 16:05:18.732][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-25 16:05:18.733][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.734][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.738][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-25 16:05:18.739][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:05:18.739][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.740][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.744][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-25 16:05:18.745][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-25 16:05:18.746][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.747][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.751][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-25 16:05:18.752][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-25 16:05:18.753][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.754][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.758][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:05:18.759][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:05:18.760][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.761][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.765][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-25 16:05:18.766][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-25 16:05:18.766][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.767][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.771][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-25 16:05:18.772][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-25 16:05:18.773][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.774][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:05:18.778][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-25 16:05:18.779][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-25 16:05:18.780][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:05:18.781][ef$get] fields variable is a list.
biodb.INFO [2025-01-25 16:05:18.787][biodb::testThat]
biodb.INFO [2025-01-25 16:05:18.788][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-01-25 16:05:18.789][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-25 16:05:18.790][biodb::testThat]
biodb.DEBUG[2025-01-25 16:05:18.807][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-01-25 16:05:18.814][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.INFO [2025-01-25 16:05:18.818][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34" for "hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34".
biodb.DEBUG[2025-01-25 16:05:18.820][self$isDownloaded] Database hmdb.metabolites has not yet been downloaded.
biodb.INFO [2025-01-25 16:05:18.821][self$download] Downloading whole database of hmdb.metabolites.
biodb.INFO [2025-01-25 16:05:18.822][private$doDownload] Downloading HMDB metabolite database at "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip" ...
biodb.DEBUG[2025-01-25 16:05:18.823][sched$downloadFile] Downloading file "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
trying URL 'http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip'
Content type 'application/zip' length 953913010 bytes (909.7 MB)
============
downloaded 228.1 MB

biodb.INFO [2025-01-25 16:06:44.513][biodb::testThat]
biodb.INFO [2025-01-25 16:06:44.515][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-01-25 16:06:44.517][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-25 16:06:44.518][biodb::testThat]
biodb.TRACE[2025-01-25 16:06:44.524][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:06:44.525][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:06:44.526][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:06:44.528][ef$get] fields variable is a list.
biodb.DEBUG[2025-01-25 16:06:44.530][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "name".
biodb.DEBUG[2025-01-25 16:06:44.563][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-01-25 16:06:44.663][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-01-25 16:06:44.665][self$isDownloaded] Database hmdb.metabolites has not yet been downloaded.
biodb.INFO [2025-01-25 16:06:44.667][self$download] Downloading whole database of hmdb.metabolites.
biodb.INFO [2025-01-25 16:06:44.669][private$doDownload] Downloading HMDB metabolite database at "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip" ...
biodb.DEBUG[2025-01-25 16:06:44.684][sched$downloadFile] Downloading file "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
trying URL 'http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip'
Content type 'application/zip' length 953913010 bytes (909.7 MB)
==============
downloaded 267.4 MB

biodb.INFO [2025-01-25 16:07:10.678][biodb::testThat]
biodb.INFO [2025-01-25 16:07:10.679][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-01-25 16:07:10.681][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-25 16:07:10.682][biodb::testThat]
biodb.DEBUG[2025-01-25 16:07:10.689][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-01-25 16:07:10.691][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-01-25 16:07:10.692][self$isDownloaded] Database hmdb.metabolites has not yet been downloaded.
biodb.INFO [2025-01-25 16:07:10.693][self$download] Downloading whole database of hmdb.metabolites.
biodb.INFO [2025-01-25 16:07:10.695][private$doDownload] Downloading HMDB metabolite database at "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip" ...
biodb.DEBUG[2025-01-25 16:07:10.696][sched$downloadFile] Downloading file "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
trying URL 'http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip'
Content type 'application/zip' length 953913010 bytes (909.7 MB)
==================
downloaded 343.1 MB

biodb.INFO [2025-01-25 16:10:32.522][biodb::testThat]
biodb.INFO [2025-01-25 16:10:32.524][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-01-25 16:10:32.525][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-25 16:10:32.526][biodb::testThat]
biodb.DEBUG[2025-01-25 16:10:32.530][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-01-25 16:10:32.531][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-01-25 16:10:32.533][self$isDownloaded] Database hmdb.metabolites has not yet been downloaded.
biodb.INFO [2025-01-25 16:10:32.534][self$download] Downloading whole database of hmdb.metabolites.
biodb.INFO [2025-01-25 16:10:32.535][private$doDownload] Downloading HMDB metabolite database at "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip" ...
biodb.DEBUG[2025-01-25 16:10:32.538][sched$downloadFile] Downloading file "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
trying URL 'http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip'
Content type 'application/zip' length 953913010 bytes (909.7 MB)
======
downloaded 117.9 MB

biodb.INFO [2025-01-25 16:11:30.200][biodb::testThat]
biodb.INFO [2025-01-25 16:11:30.201][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-01-25 16:11:30.203][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-25 16:11:30.204][biodb::testThat]
biodb.INFO [2025-01-25 16:11:30.212][biodb::testThat]
biodb.INFO [2025-01-25 16:11:30.213][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-01-25 16:11:30.214][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-25 16:11:30.214][biodb::testThat]
biodb.INFO [2025-01-25 16:11:30.221][biodb::testThat]
biodb.INFO [2025-01-25 16:11:30.222][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-01-25 16:11:30.223][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-25 16:11:30.224][biodb::testThat]
biodb.DEBUG[2025-01-25 16:11:30.227][function(conn, opt)] Trying to download "http://www.hmdb.ca/metabolites/HMDB0000001".
biodb.DEBUG[2025-01-25 16:11:37.156][getUrlContent] Use RCurl for downloading content of URL http://www.hmdb.ca/metabolites/HMDB0000001.
biodb.INFO [2025-01-25 16:11:37.189][biodb::testThat]
biodb.INFO [2025-01-25 16:11:37.190][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-01-25 16:11:37.191][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-25 16:11:37.192][biodb::testThat]
biodb.DEBUG[2025-01-25 16:11:37.790][getUrlContent] Use RCurl for downloading content of URL http://www.hmdb.ca/structures/HMDB0000001/image.png.
biodb.TRACE[2025-01-25 16:11:37.863][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:11:37.866][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:11:37.867][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:11:37.869][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:11:37.871][ef$get] Asked field names are: description.
biodb.TRACE[2025-01-25 16:11:37.873][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-01-25 16:11:37.875][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:11:37.876][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:11:37.878][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-25 16:11:37.879][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-25 16:11:37.881][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:11:37.882][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:11:37.883][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:11:37.885][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:11:37.896][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:11:37.897][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:11:37.898][ef$get] Asked field names are: description.
biodb.TRACE[2025-01-25 16:11:37.899][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-01-25 16:11:37.900][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:11:37.900][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:11:37.901][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-25 16:11:37.902][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-25 16:11:37.903][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:11:37.904][ef$get] fields variable is a list.
biodb.INFO [2025-01-25 16:11:37.905][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-01-25 16:11:37.907][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler
biodb.INFO [2025-01-25 16:11:37.908][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2025-01-25 16:11:37.909][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-01-25 16:11:37.910][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:11:37.911][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:11:37.912][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:11:37.912][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:11:37.913][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:11:37.914][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 4 | WARN 8 | SKIP 0 | PASS 113 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_long_100_generic.R:42:1'): RT unit is defined when there is an RT value. ──
Error in `utils::download.file(url = url, destfile = dest.file, mode = "wb", 
    method = "auto", cacheOK = FALSE, quiet = FALSE)`: download from 'http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip' failed
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
 3.   └─conn$getBiodb()$getFactory()$getEntry(...)
 4.     └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
 5.       └─conn$getEntryContent(ids)
 6.         └─self$download()
 7.           └─private$doDownload()
 8.             └─sched$downloadFile(url = zip.url, dest.file = tmpFile)
 9.               └─utils::download.file(...)
── Error ('test_long_100_generic.R:42:1'): We can search for an entry by searchable field ──
Error in `utils::download.file(url = url, destfile = dest.file, mode = "wb", 
    method = "auto", cacheOK = FALSE, quiet = FALSE)`: download from 'http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip' failed
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
  3.   └─conn$getEntry(id, drop = TRUE)
  4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
  5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  6.         └─conn$getEntryContent(ids)
  7.           └─self$download()
  8.             └─private$doDownload()
  9.               └─sched$downloadFile(url = zip.url, dest.file = tmpFile)
 10.                 └─utils::download.file(...)
── Error ('test_long_100_generic.R:42:1'): We can search for an entry by name. ──
Error in `utils::download.file(url = url, destfile = dest.file, mode = "wb", 
    method = "auto", cacheOK = FALSE, quiet = FALSE)`: download from 'http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip' failed
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
  3.   └─conn$getEntry(id, drop = TRUE)
  4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
  5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  6.         └─conn$getEntryContent(ids)
  7.           └─self$download()
  8.             └─private$doDownload()
  9.               └─sched$downloadFile(url = zip.url, dest.file = tmpFile)
 10.                 └─utils::download.file(...)
── Error ('test_long_100_generic.R:42:1'): We can load an entry from the database. ──
Error in `utils::download.file(url = url, destfile = dest.file, mode = "wb", 
    method = "auto", cacheOK = FALSE, quiet = FALSE)`: download from 'http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip' failed
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
  3.   └─opt$refEntries$getRealEntry(id)
  4.     └─self$getRealEntries(ids = id)
  5.       └─private$bdb$getFactory()$getEntry(...)
  6.         └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  7.           └─conn$getEntryContent(ids)
  8.             └─self$download()
  9.               └─private$doDownload()
 10.                 └─sched$downloadFile(url = zip.url, dest.file = tmpFile)
 11.                   └─utils::download.file(...)

[ FAIL 4 | WARN 8 | SKIP 0 | PASS 113 ]
Error: Test failures
Execution halted

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   /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_1.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc-longtests/meat/biodbHmdb.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* 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 24.04.1 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 ‘1.13.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbHmdb’ can be installed ... OK
* 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:
    1. ├─base::do.call(fct, params)
    2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
    3.   └─opt$refEntries$getRealEntry(id)
    4.     └─self$getRealEntries(ids = id)
    5.       └─private$bdb$getFactory()$getEntry(...)
    6.         └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
    7.           └─conn$getEntryContent(ids)
    8.             └─self$download()
    9.               └─private$doDownload()
   10.                 └─sched$downloadFile(url = zip.url, dest.file = tmpFile)
   11.                   └─utils::download.file(...)
  
  [ FAIL 4 | WARN 8 | SKIP 0 | PASS 113 ]
  Error: Test failures
  Execution halted
* DONE

Status: 1 ERROR, 1 WARNING, 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 ‘1.13.0’
** 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  -DR_NO_REMAP -c EntryMaker.cpp -o EntryMaker.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  -DR_NO_REMAP -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  -DR_NO_REMAP -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  -DR_NO_REMAP -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  -DR_NO_REMAP -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  -DR_NO_REMAP -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  -DR_NO_REMAP -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  -DR_NO_REMAP -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  -DR_NO_REMAP -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  -DR_NO_REMAP -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  -DR_NO_REMAP -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)