Back to Long Tests report for BioC 3.20

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

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4746
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4494
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4517
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 8/32HostnameOS / ArchCHECK
biodbHmdb 1.12.0  (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: RELEASE_3_20
git_last_commit: 0eb718c
git_last_commit_date: 2024-10-29 11:06:39 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  WARNINGS  
palomino8Windows Server 2022 Datacenter / x64  WARNINGS  
merida1macOS 12.7.5 Monterey / x86_64  WARNINGS  

CHECK results for biodbHmdb on nebbiolo2

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: 1.12.0
Command: /home/biocbuild/bbs-3.20-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_1.12.0.tar.gz
StartedAt: 2025-01-25 16:02:39 -0500 (Sat, 25 Jan 2025)
EndedAt: 2025-01-25 16:03:56 -0500 (Sat, 25 Jan 2025)
EllapsedTime: 77.0 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: biodbHmdb.Rcheck
Warnings: 2

Tests output

biodbHmdb.Rcheck/tests/testthat.Rout


R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbHmdb)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbHmdb")
biodb.INFO [2025-01-25 16:03:40.194][biodb::testContext]
biodb.INFO [2025-01-25 16:03:40.196][biodb::testContext] ********************************************************************************
biodb.INFO [2025-01-25 16:03:40.197][biodb::testContext] Test context - Generic long tests
biodb.INFO [2025-01-25 16:03:40.198][biodb::testContext] ********************************************************************************
biodb.INFO [2025-01-25 16:03:40.199][biodb::testContext]
biodb.INFO [2025-01-25 16:03:40.204][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2025-01-25 16:03:40.206][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-01-25 16:03:40.212][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-25 16:03:40.213][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-01-25 16:03:40.214][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-01-25 16:03:40.215][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:40.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:40.217][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:40.218][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-01-25 16:03:40.234][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-01-25 16:03:40.235][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:40.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:40.237][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:40.238][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-01-25 16:03:40.238][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-01-25 16:03:40.239][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:40.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:40.241][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:40.242][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-01-25 16:03:40.243][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-01-25 16:03:40.244][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-01-25 16:03:40.244][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:40.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:40.246][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:03:40.247][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-01-25 16:03:40.248][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-01-25 16:03:40.249][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-01-25 16:03:40.250][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:40.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:40.251][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:40.252][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-01-25 16:03:40.253][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-01-25 16:03:40.254][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:40.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:40.255][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:40.256][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-01-25 16:03:40.257][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-01-25 16:03:40.258][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-01-25 16:03:40.259][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:40.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:40.260][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:40.261][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-01-25 16:03:40.262][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-01-25 16:03:40.263][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:40.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:40.265][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:03:40.266][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-01-25 16:03:40.266][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-01-25 16:03:40.267][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-01-25 16:03:40.268][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:40.269][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:40.270][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:40.271][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-01-25 16:03:40.272][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-01-25 16:03:40.273][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-01-25 16:03:40.273][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-01-25 16:03:40.274][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-01-25 16:03:40.275][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-01-25 16:03:40.276][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:40.277][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:40.278][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:03:40.279][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-01-25 16:03:40.280][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-01-25 16:03:40.280][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:40.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:40.282][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:40.283][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-01-25 16:03:40.284][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-01-25 16:03:40.285][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:40.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:40.286][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:40.287][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-01-25 16:03:40.288][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-01-25 16:03:40.289][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:40.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:40.290][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:40.291][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-01-25 16:03:40.292][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-01-25 16:03:40.293][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:40.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:40.295][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:03:40.296][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-01-25 16:03:40.296][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-01-25 16:03:40.297][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:40.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:40.299][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:40.300][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-01-25 16:03:40.301][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-01-25 16:03:40.306][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-01-25 16:03:40.307][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:40.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:40.308][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:03:40.309][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-01-25 16:03:40.310][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-01-25 16:03:40.311][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-01-25 16:03:40.312][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:40.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:40.313][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:40.317][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-01-25 16:03:40.347][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-25 16:03:40.367][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-01-25 16:03:40.368][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-25 16:03:40.369][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-25 16:03:40.370][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-25 16:03:40.371][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-25 16:03:40.372][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-25 16:03:40.372][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-25 16:03:40.373][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-01-25 16:03:40.374][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-25 16:03:40.375][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-25 16:03:40.376][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-01-25 16:03:40.377][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-25 16:03:40.378][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:03:40.379][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-25 16:03:40.380][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-25 16:03:40.380][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-01-25 16:03:40.380][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-01-25 16:03:40.380][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-01-25 16:03:40.380][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-01-25 16:03:40.381][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-25 16:03:40.382][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-25 16:03:40.382][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-25 16:03:40.383][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-25 16:03:40.384][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-25 16:03:40.385][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-25 16:03:40.386][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-25 16:03:40.387][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:03:40.388][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-25 16:03:40.389][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-25 16:03:40.389][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-25 16:03:40.390][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:03:40.391][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-01-25 16:03:40.393][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-25 16:03:40.394][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-01-25 16:03:40.395][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-25 16:03:40.396][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-25 16:03:40.397][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-25 16:03:40.398][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-25 16:03:40.398][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-25 16:03:40.399][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-25 16:03:40.400][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-01-25 16:03:40.401][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-25 16:03:40.402][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-25 16:03:40.403][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-01-25 16:03:40.404][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-25 16:03:40.405][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:03:40.406][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-25 16:03:40.407][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-25 16:03:40.407][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-01-25 16:03:40.407][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-01-25 16:03:40.407][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-01-25 16:03:40.407][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-01-25 16:03:40.408][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-25 16:03:40.409][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-25 16:03:40.409][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-25 16:03:40.410][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-25 16:03:40.411][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-25 16:03:40.412][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-25 16:03:40.413][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-25 16:03:40.414][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:03:40.415][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-25 16:03:40.415][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-25 16:03:40.416][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-25 16:03:40.417][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:03:40.418][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-01-25 16:03:40.420][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-01-25 16:03:40.421][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-01-25 16:03:40.422][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-25 16:03:40.423][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-25 16:03:40.424][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-25 16:03:40.424][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-25 16:03:40.425][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-25 16:03:40.426][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-25 16:03:40.427][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-01-25 16:03:40.428][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-25 16:03:40.429][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-01-25 16:03:40.430][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-01-25 16:03:40.431][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-25 16:03:40.432][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:03:40.433][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-25 16:03:40.434][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:03:40.434][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-25 16:03:40.435][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-25 16:03:40.436][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-25 16:03:40.437][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-25 16:03:40.438][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-25 16:03:40.439][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-25 16:03:40.440][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-25 16:03:40.440][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:03:40.441][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-25 16:03:40.442][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-25 16:03:40.443][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-25 16:03:40.444][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:03:40.445][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-01-25 16:03:40.447][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-01-25 16:03:40.447][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-01-25 16:03:40.448][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-25 16:03:40.449][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-25 16:03:40.450][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-25 16:03:40.451][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-25 16:03:40.452][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-25 16:03:40.453][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-25 16:03:40.454][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-01-25 16:03:40.455][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-25 16:03:40.456][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-01-25 16:03:40.457][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-01-25 16:03:40.457][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-25 16:03:40.458][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:03:40.459][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-25 16:03:40.460][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:03:40.461][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-25 16:03:40.462][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-25 16:03:40.463][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-25 16:03:40.464][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-25 16:03:40.465][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-25 16:03:40.465][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-25 16:03:40.466][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-25 16:03:40.467][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:03:40.468][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-25 16:03:40.469][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-25 16:03:40.470][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-25 16:03:40.471][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:03:40.474][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-25 16:03:40.475][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:40.476][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:03:40.476][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:40.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:40.478][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 16:03:40.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:40.480][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:03:40.480][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:40.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:40.482][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 16:03:40.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:40.484][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:03:40.484][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:40.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:40.486][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 16:03:40.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:40.488][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:03:40.488][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:40.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:40.490][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 16:03:40.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:40.492][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:03:40.493][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:40.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:40.494][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 16:03:40.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:40.496][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:40.496][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:40.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:40.498][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 16:03:40.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:40.500][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:03:40.500][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:40.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:40.502][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 16:03:40.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:40.504][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:03:40.505][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:40.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:40.506][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 16:03:40.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:40.508][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:03:40.509][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:40.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:40.510][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:03:40.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:40.512][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:40.513][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:40.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:40.514][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 16:03:40.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:40.516][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:03:40.517][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:40.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:40.518][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:03:40.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:40.520][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:40.521][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:40.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:40.522][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 16:03:40.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:40.524][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:03:40.525][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:40.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:40.530][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:03:40.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:40.531][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:40.532][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:40.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:40.534][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 16:03:40.535][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:40.535][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:03:40.536][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:40.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:40.538][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:03:40.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:40.539][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:03:40.540][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:40.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:40.542][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 16:03:40.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:40.543][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:03:40.544][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:40.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:40.546][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:03:40.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:40.547][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:03:40.548][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-01-25 16:03:40.552][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-01-25 16:03:40.554][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-01-25 16:03:40.555][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-01-25 16:03:40.556][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-01-25 16:03:40.558][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-01-25 16:03:40.559][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-01-25 16:03:40.560][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-01-25 16:03:40.561][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-01-25 16:03:40.563][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-01-25 16:03:40.564][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-01-25 16:03:40.565][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-01-25 16:03:40.566][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-01-25 16:03:40.568][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-01-25 16:03:40.569][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-01-25 16:03:40.570][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-01-25 16:03:40.571][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-01-25 16:03:40.573][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-01-25 16:03:40.574][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-01-25 16:03:40.575][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-01-25 16:03:40.577][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-01-25 16:03:40.578][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-01-25 16:03:40.579][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-01-25 16:03:40.580][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-01-25 16:03:40.582][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-01-25 16:03:40.583][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-01-25 16:03:40.584][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-01-25 16:03:40.585][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-01-25 16:03:40.587][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-01-25 16:03:40.588][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-01-25 16:03:40.589][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-01-25 16:03:40.591][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-01-25 16:03:40.592][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-01-25 16:03:40.593][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-01-25 16:03:40.594][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-01-25 16:03:40.596][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-01-25 16:03:40.597][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-01-25 16:03:40.598][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-01-25 16:03:40.599][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-01-25 16:03:40.601][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-01-25 16:03:40.602][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-01-25 16:03:40.603][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-01-25 16:03:40.604][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-01-25 16:03:40.606][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-01-25 16:03:40.607][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-01-25 16:03:40.608][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-01-25 16:03:40.610][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-01-25 16:03:40.611][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-01-25 16:03:40.612][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-01-25 16:03:40.613][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-01-25 16:03:40.615][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-01-25 16:03:40.616][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-01-25 16:03:40.617][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-01-25 16:03:40.618][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-01-25 16:03:40.620][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-01-25 16:03:40.621][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-01-25 16:03:40.622][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-01-25 16:03:40.630][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-01-25 16:03:40.632][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-01-25 16:03:40.633][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-01-25 16:03:40.635][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-01-25 16:03:40.636][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-01-25 16:03:40.638][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-01-25 16:03:40.639][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-01-25 16:03:40.641][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-01-25 16:03:40.642][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-01-25 16:03:40.644][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-01-25 16:03:40.645][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-01-25 16:03:40.646][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-01-25 16:03:40.648][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-01-25 16:03:40.649][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-01-25 16:03:40.651][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-01-25 16:03:40.652][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-01-25 16:03:40.654][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-01-25 16:03:40.655][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-01-25 16:03:40.656][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-01-25 16:03:40.658][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-01-25 16:03:40.659][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-01-25 16:03:40.661][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-01-25 16:03:40.662][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-01-25 16:03:40.663][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-01-25 16:03:40.665][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-01-25 16:03:40.666][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-01-25 16:03:40.673][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-01-25 16:03:40.675][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2025-01-25 16:03:40.679][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-25 16:03:40.679][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:40.680][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 16:03:40.681][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:40.682][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:03:40.687][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:40.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:03:40.689][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:03:40.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:40.691][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 16:03:40.691][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:40.692][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:40.693][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:40.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:03:40.695][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:03:40.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:40.697][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:03:40.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:40.699][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:03:40.699][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:40.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:03:40.701][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:03:40.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:40.703][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:03:40.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:40.705][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:40.706][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:40.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:03:40.721][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:03:40.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:40.723][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:03:40.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:40.725][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:40.725][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:40.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:03:40.727][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:03:40.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:40.729][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:03:40.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:40.731][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:40.732][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:40.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:03:40.733][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:03:40.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:40.735][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 16:03:40.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:40.737][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:40.738][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:40.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:03:40.740][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:03:40.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:40.741][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 16:03:40.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:40.743][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:03:40.744][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:40.745][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:03:40.746][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:03:40.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:40.748][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:03:40.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:40.750][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:40.750][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:40.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:03:40.752][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:03:40.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:40.754][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 16:03:40.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:40.756][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:03:40.757][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:40.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:03:40.758][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:03:40.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:40.760][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 16:03:40.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:40.762][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:03:40.763][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:40.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:03:40.764][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:03:40.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:40.766][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 16:03:40.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:40.768][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:03:40.769][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:40.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:03:40.770][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:03:40.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:40.772][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 16:03:40.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:40.774][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:03:40.775][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:40.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:03:40.777][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:03:40.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:40.778][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 16:03:40.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:40.780][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:03:40.781][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:40.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:03:40.783][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:03:40.783][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:40.784][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 16:03:40.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:40.786][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:03:40.787][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:40.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:03:40.789][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:03:40.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:40.790][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 16:03:40.791][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:40.792][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:03:40.793][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:40.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:03:40.795][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:03:40.796][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:40.796][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 16:03:40.797][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:40.798][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:03:40.799][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:40.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:03:40.801][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:03:40.802][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:40.803][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 16:03:40.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:40.804][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 16:03:40.805][biodb$getConfig()$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-01-25 16:03:40.806][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:40.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:03:40.808][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:03:40.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:40.810][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:03:40.810][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:40.811][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:40.813][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/definitions.yml".
biodb.DEBUG[2025-01-25 16:03:40.822][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2025-01-25 16:03:40.824][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-25 16:03:40.825][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-01-25 16:03:40.826][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-25 16:03:40.827][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-25 16:03:40.828][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-01-25 16:03:40.829][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2025-01-25 16:03:40.829][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-01-25 16:03:40.830][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-25 16:03:40.831][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-01-25 16:03:40.832][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-25 16:03:40.833][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-25 16:03:40.834][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2025-01-25 16:03:40.835][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-25 16:03:40.836][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2025-01-25 16:03:40.836][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2025-01-25 16:03:40.836][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2025-01-25 16:03:40.836][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2025-01-25 16:03:40.836][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2025-01-25 16:03:40.836][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2025-01-25 16:03:40.836][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2025-01-25 16:03:40.836][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2025-01-25 16:03:40.836][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2025-01-25 16:03:40.836][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2025-01-25 16:03:40.836][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2025-01-25 16:03:40.836][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2025-01-25 16:03:40.836][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2025-01-25 16:03:40.836][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2025-01-25 16:03:40.836][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2025-01-25 16:03:40.836][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2025-01-25 16:03:40.836][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2025-01-25 16:03:40.836][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2025-01-25 16:03:40.837][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-01-25 16:03:40.838][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-25 16:03:40.838][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2025-01-25 16:03:40.838][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2025-01-25 16:03:40.839][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-01-25 16:03:40.840][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-25 16:03:40.840][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-25 16:03:40.841][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-25 16:03:40.842][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-25 16:03:40.843][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-25 16:03:40.844][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-25 16:03:40.845][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2025-01-25 16:03:40.845][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2025-01-25 16:03:40.846][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-25 16:03:40.846][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-25 16:03:40.847][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-01-25 16:03:40.848][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:03:40.854][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2025-01-25 16:03:40.855][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-01-25 16:03:40.856][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-01-25 16:03:40.858][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-01-25 16:03:40.859][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-01-25 16:03:40.880][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2025-01-25 16:03:40.881][initialize] Register connector hmdb.metabolites with the request scheduler
biodb.DEBUG[2025-01-25 16:03:40.885][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites.
biodb.DEBUG[2025-01-25 16:03:40.889][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2025-01-25 16:03:40.892][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-01-25 16:03:40.893][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-01-25 16:03:40.894][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca".
biodb.DEBUG[2025-01-25 16:03:40.924][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.INFO [2025-01-25 16:03:40.932][biodb::testThat]
biodb.INFO [2025-01-25 16:03:40.933][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-01-25 16:03:40.934][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-25 16:03:40.935][biodb::testThat]
biodb.TRACE[2025-01-25 16:03:40.938][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.20-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/testref/entry-hmdb.metabolites-HMDB0000001-content.xml".
biodb.DEBUG[2025-01-25 16:03:40.940][biodb$getFactory()$createEntryFromCo ...] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-01-25 16:03:40.943][biodb$getFactory()$createEntryFromCo ...] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-01-25 16:03:40.950][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-25 16:03:40.951][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:03:40.952][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:03:40.963][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:40.963][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 16:03:40.964][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:40.965][FUN] Functions in observer BiodbConfig: [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 16:03:40.976][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:03:40.976][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:03:40.977][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:40.978][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:40.980][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:03:40.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:03:40.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:40.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:40.995][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-25 16:03:40.996][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-25 16:03:40.996][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:40.997][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.022][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-25 16:03:41.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-25 16:03:41.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.026][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-25 16:03:41.027][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-25 16:03:41.027][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.028][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.030][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-25 16:03:41.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-25 16:03:41.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.033][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-25 16:03:41.034][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-25 16:03:41.035][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.036][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.037][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-25 16:03:41.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-25 16:03:41.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.041][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-25 16:03:41.042][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-25 16:03:41.043][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.044][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.045][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-25 16:03:41.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-25 16:03:41.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.049][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-25 16:03:41.050][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-25 16:03:41.051][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.051][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.053][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-25 16:03:41.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-25 16:03:41.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.056][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-25 16:03:41.057][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-25 16:03:41.058][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.059][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.060][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-25 16:03:41.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-25 16:03:41.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.064][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-25 16:03:41.065][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-25 16:03:41.066][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.067][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.068][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-25 16:03:41.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-25 16:03:41.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.072][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-25 16:03:41.073][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-25 16:03:41.074][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.075][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.076][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-25 16:03:41.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-25 16:03:41.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.086][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-25 16:03:41.087][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-25 16:03:41.088][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.089][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.090][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-25 16:03:41.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-25 16:03:41.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.094][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-25 16:03:41.095][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-25 16:03:41.095][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.096][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.097][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-25 16:03:41.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-25 16:03:41.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.101][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-25 16:03:41.102][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-25 16:03:41.103][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.104][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.105][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-25 16:03:41.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-25 16:03:41.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.109][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-25 16:03:41.110][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:03:41.111][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.112][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.113][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-25 16:03:41.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:03:41.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.117][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-25 16:03:41.117][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-25 16:03:41.118][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.119][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.120][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-25 16:03:41.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-25 16:03:41.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.124][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:03:41.125][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:03:41.126][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.127][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.128][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:03:41.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:03:41.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.132][ef$get] Asked field names are: description.
biodb.TRACE[2025-01-25 16:03:41.133][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-01-25 16:03:41.134][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.134][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.135][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-25 16:03:41.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-25 16:03:41.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.139][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-25 16:03:41.140][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-25 16:03:41.141][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.142][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.143][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-25 16:03:41.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-25 16:03:41.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.147][ef$get] Asked field names are: super.class.
biodb.TRACE[2025-01-25 16:03:41.148][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-25 16:03:41.149][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.150][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.151][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2025-01-25 16:03:41.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-25 16:03:41.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.155][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:03:41.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:03:41.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.158][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:03:41.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:03:41.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.162][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:03:41.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:03:41.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.196][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-25 16:03:41.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-25 16:03:41.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.200][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-25 16:03:41.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-25 16:03:41.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.204][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-25 16:03:41.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-25 16:03:41.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.207][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-25 16:03:41.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-25 16:03:41.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.211][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-25 16:03:41.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-25 16:03:41.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.218][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-25 16:03:41.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-25 16:03:41.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.222][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-25 16:03:41.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-25 16:03:41.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.225][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-25 16:03:41.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-25 16:03:41.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.229][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-25 16:03:41.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-25 16:03:41.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.233][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-25 16:03:41.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-25 16:03:41.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.236][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-25 16:03:41.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-25 16:03:41.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.240][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-25 16:03:41.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-25 16:03:41.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.243][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-25 16:03:41.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-25 16:03:41.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.247][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-25 16:03:41.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-25 16:03:41.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.251][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-25 16:03:41.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-25 16:03:41.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.254][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-25 16:03:41.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-25 16:03:41.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.258][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-25 16:03:41.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-25 16:03:41.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.262][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-25 16:03:41.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-25 16:03:41.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.265][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-01-25 16:03:41.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-25 16:03:41.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.269][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-01-25 16:03:41.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-25 16:03:41.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.273][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-01-25 16:03:41.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-25 16:03:41.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.276][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-25 16:03:41.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-25 16:03:41.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.280][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-25 16:03:41.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-25 16:03:41.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.283][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-25 16:03:41.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-25 16:03:41.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.287][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-25 16:03:41.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-25 16:03:41.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.291][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-25 16:03:41.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-25 16:03:41.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.294][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-25 16:03:41.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-25 16:03:41.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.298][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-25 16:03:41.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-25 16:03:41.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.302][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-25 16:03:41.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-25 16:03:41.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.305][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-25 16:03:41.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-25 16:03:41.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.309][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-25 16:03:41.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:03:41.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.312][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-25 16:03:41.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:03:41.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.316][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-25 16:03:41.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:03:41.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.320][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-25 16:03:41.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-25 16:03:41.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.323][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-25 16:03:41.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-25 16:03:41.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.327][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-25 16:03:41.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-25 16:03:41.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.331][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-25 16:03:41.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-25 16:03:41.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.334][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-25 16:03:41.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-25 16:03:41.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.338][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-25 16:03:41.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-25 16:03:41.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.341][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:03:41.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:03:41.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.345][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:03:41.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:03:41.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.349][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:03:41.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:03:41.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.356][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-25 16:03:41.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-25 16:03:41.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.359][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-25 16:03:41.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-25 16:03:41.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.363][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-25 16:03:41.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-25 16:03:41.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.366][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-25 16:03:41.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-25 16:03:41.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.370][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-25 16:03:41.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-25 16:03:41.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.374][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-25 16:03:41.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-25 16:03:41.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.377][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-25 16:03:41.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-25 16:03:41.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.381][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-25 16:03:41.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-25 16:03:41.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.385][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-25 16:03:41.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-25 16:03:41.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.388][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-01-25 16:03:41.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:03:41.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.392][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-25 16:03:41.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:03:41.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.396][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-25 16:03:41.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:03:41.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.399][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-25 16:03:41.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:03:41.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.403][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-01-25 16:03:41.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:03:41.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.423][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:03:41.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:03:41.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.426][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:03:41.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:03:41.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.430][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:03:41.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:03:41.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.434][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:03:41.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:03:41.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.437][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:03:41.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:03:41.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.441][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-01-25 16:03:41.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-01-25 16:03:41.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.445][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-01-25 16:03:41.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-01-25 16:03:41.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.448][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:03:41.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:03:41.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.452][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-01-25 16:03:41.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-01-25 16:03:41.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.456][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:03:41.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:03:41.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.459][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:03:41.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:03:41.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.463][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:03:41.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:03:41.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.467][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:03:41.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:03:41.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.470][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:03:41.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:03:41.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.474][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:03:41.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:03:41.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-25 16:03:41.477][biodb$getFactory()$createEntryFromCo ...] Accession numbers: HMDB0000001.
biodb.TRACE[2025-01-25 16:03:41.480][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-25 16:03:41.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-25 16:03:41.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.483][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-25 16:03:41.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-25 16:03:41.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.490][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-01-25 16:03:41.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-01-25 16:03:41.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.494][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-01-25 16:03:41.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-01-25 16:03:41.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.511][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:03:41.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:03:41.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.525][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-01-25 16:03:41.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-01-25 16:03:41.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.532][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:03:41.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:03:41.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.536][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:03:41.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:03:41.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.539][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:03:41.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:03:41.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.544][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:03:41.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:03:41.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.548][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:03:41.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:03:41.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.552][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:03:41.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:03:41.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.555][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-01-25 16:03:41.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-01-25 16:03:41.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.559][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-01-25 16:03:41.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-01-25 16:03:41.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.563][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-01-25 16:03:41.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-01-25 16:03:41.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.572][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:03:41.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:03:41.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.576][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:03:41.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:03:41.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.579][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:03:41.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:03:41.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.583][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:03:41.584][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:03:41.585][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.586][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.587][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:03:41.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:03:41.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.597][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-25 16:03:41.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-25 16:03:41.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.600][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-25 16:03:41.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-25 16:03:41.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.604][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-25 16:03:41.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-25 16:03:41.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.607][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-25 16:03:41.608][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-25 16:03:41.609][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.610][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.611][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-25 16:03:41.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-25 16:03:41.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.621][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-25 16:03:41.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-25 16:03:41.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.629][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-25 16:03:41.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-25 16:03:41.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.632][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-25 16:03:41.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-25 16:03:41.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.636][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-25 16:03:41.637][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-25 16:03:41.638][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.639][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.639][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-25 16:03:41.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-25 16:03:41.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.649][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-25 16:03:41.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-25 16:03:41.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.653][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-25 16:03:41.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-25 16:03:41.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.657][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-25 16:03:41.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-25 16:03:41.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.660][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-25 16:03:41.661][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-25 16:03:41.662][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.663][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.664][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-25 16:03:41.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-25 16:03:41.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.674][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-25 16:03:41.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-25 16:03:41.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.677][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-25 16:03:41.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-25 16:03:41.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.681][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-25 16:03:41.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-25 16:03:41.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.685][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-25 16:03:41.686][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-25 16:03:41.686][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.687][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.688][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-25 16:03:41.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-25 16:03:41.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.698][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-25 16:03:41.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-25 16:03:41.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.702][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-25 16:03:41.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-25 16:03:41.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.705][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-25 16:03:41.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-25 16:03:41.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.709][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-25 16:03:41.710][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-25 16:03:41.711][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.712][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.713][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-25 16:03:41.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-25 16:03:41.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.722][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:03:41.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:03:41.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.726][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:03:41.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:03:41.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.730][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:03:41.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:03:41.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.733][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:03:41.734][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:03:41.735][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.736][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.737][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:03:41.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:03:41.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.747][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-25 16:03:41.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-25 16:03:41.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.751][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-25 16:03:41.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-25 16:03:41.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.754][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-25 16:03:41.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-25 16:03:41.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.762][ef$get] Asked field names are: description.
biodb.TRACE[2025-01-25 16:03:41.763][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-01-25 16:03:41.763][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.764][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.765][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-25 16:03:41.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-25 16:03:41.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.775][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-25 16:03:41.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-25 16:03:41.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.779][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-25 16:03:41.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-25 16:03:41.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.783][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-25 16:03:41.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-25 16:03:41.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.786][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-25 16:03:41.787][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-25 16:03:41.788][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.789][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.790][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-25 16:03:41.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-25 16:03:41.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.800][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-25 16:03:41.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-25 16:03:41.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.804][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-25 16:03:41.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-25 16:03:41.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.807][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-25 16:03:41.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-25 16:03:41.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.811][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-25 16:03:41.812][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-25 16:03:41.813][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.813][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.814][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-25 16:03:41.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-25 16:03:41.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.824][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-25 16:03:41.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-25 16:03:41.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.828][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-25 16:03:41.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-25 16:03:41.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.831][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-25 16:03:41.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-25 16:03:41.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.835][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-25 16:03:41.836][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-25 16:03:41.837][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.838][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.839][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-25 16:03:41.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-25 16:03:41.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.848][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-01-25 16:03:41.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-25 16:03:41.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.852][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-01-25 16:03:41.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-25 16:03:41.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.856][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-01-25 16:03:41.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-25 16:03:41.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.859][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-01-25 16:03:41.860][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-25 16:03:41.861][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.862][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.863][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-01-25 16:03:41.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-25 16:03:41.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.873][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-25 16:03:41.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-25 16:03:41.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.876][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-25 16:03:41.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-25 16:03:41.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.880][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-25 16:03:41.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-25 16:03:41.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.883][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-25 16:03:41.884][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-25 16:03:41.885][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.886][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.887][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-25 16:03:41.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-25 16:03:41.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.900][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-25 16:03:41.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-25 16:03:41.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.904][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-25 16:03:41.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-25 16:03:41.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.908][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-25 16:03:41.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-25 16:03:41.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.911][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-25 16:03:41.912][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-25 16:03:41.913][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.914][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.915][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-25 16:03:41.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-25 16:03:41.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.925][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-25 16:03:41.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-25 16:03:41.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.929][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-25 16:03:41.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-25 16:03:41.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.932][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-25 16:03:41.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-25 16:03:41.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.936][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-25 16:03:41.937][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-25 16:03:41.938][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.939][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.940][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-25 16:03:41.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-25 16:03:41.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.950][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-25 16:03:41.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-25 16:03:41.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.953][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-25 16:03:41.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-25 16:03:41.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.957][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-25 16:03:41.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-25 16:03:41.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.960][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-25 16:03:41.961][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-25 16:03:41.962][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.963][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.964][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-25 16:03:41.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-25 16:03:41.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.974][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-25 16:03:41.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:03:41.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.978][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-25 16:03:41.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:03:41.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.981][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-25 16:03:41.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:03:41.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.985][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-25 16:03:41.986][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:03:41.987][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.988][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.988][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-25 16:03:41.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:03:41.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:41.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:41.998][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-25 16:03:41.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-25 16:03:42.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.002][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-25 16:03:42.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-25 16:03:42.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.006][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-25 16:03:42.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-25 16:03:42.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.009][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-25 16:03:42.010][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-25 16:03:42.011][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.012][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.013][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-25 16:03:42.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-25 16:03:42.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.023][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:03:42.024][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:03:42.028][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.029][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.033][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-25 16:03:42.034][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-25 16:03:42.035][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.036][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.040][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-25 16:03:42.041][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-25 16:03:42.042][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.042][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.046][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-25 16:03:42.047][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-25 16:03:42.048][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.049][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.053][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-25 16:03:42.054][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-25 16:03:42.055][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.056][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.059][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-25 16:03:42.060][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-25 16:03:42.061][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.062][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.066][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-25 16:03:42.067][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-25 16:03:42.068][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.069][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.072][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-01-25 16:03:42.073][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-25 16:03:42.074][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.075][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.079][ef$get] Asked field names are: description.
biodb.TRACE[2025-01-25 16:03:42.080][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-01-25 16:03:42.081][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.082][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.085][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-25 16:03:42.086][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-25 16:03:42.087][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.088][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.092][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-25 16:03:42.093][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-25 16:03:42.094][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.095][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.098][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-25 16:03:42.099][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:03:42.100][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.101][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.105][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-25 16:03:42.106][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-25 16:03:42.107][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.108][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.111][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-25 16:03:42.112][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-25 16:03:42.113][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.114][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.118][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:03:42.119][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:03:42.120][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.121][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.125][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-25 16:03:42.126][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-25 16:03:42.126][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.127][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.131][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-25 16:03:42.132][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-25 16:03:42.133][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.134][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.138][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-25 16:03:42.139][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-25 16:03:42.139][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.140][ef$get] fields variable is a list.
biodb.INFO [2025-01-25 16:03:42.147][biodb::testThat]
biodb.INFO [2025-01-25 16:03:42.147][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-01-25 16:03:42.148][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-25 16:03:42.149][biodb::testThat]
biodb.DEBUG[2025-01-25 16:03:42.166][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-01-25 16:03:42.173][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-01-25 16:03:42.177][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-25 16:03:42.178][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2025-01-25 16:03:42.180][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000001".
biodb.TRACE[2025-01-25 16:03:42.181][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-25 16:03:42.184][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000001.xml".
biodb.DEBUG[2025-01-25 16:03:42.185][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2025-01-25 16:03:42.207][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-01-25 16:03:42.208][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-01-25 16:03:42.210][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-25 16:03:42.210][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:03:42.211][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:03:42.216][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:42.216][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:03:42.217][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:42.218][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-25 16:03:42.221][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:03:42.222][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:03:42.223][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.224][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.225][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:03:42.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:03:42.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.229][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-25 16:03:42.230][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-25 16:03:42.231][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.232][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.233][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-25 16:03:42.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-25 16:03:42.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.237][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-25 16:03:42.238][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-25 16:03:42.238][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.239][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.241][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-25 16:03:42.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-25 16:03:42.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.244][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-25 16:03:42.245][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-25 16:03:42.246][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.247][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.248][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-25 16:03:42.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-25 16:03:42.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.252][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-25 16:03:42.253][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-25 16:03:42.254][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.255][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.256][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-25 16:03:42.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-25 16:03:42.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.260][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-25 16:03:42.261][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-25 16:03:42.261][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.262][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.264][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-25 16:03:42.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-25 16:03:42.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.267][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-25 16:03:42.268][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-25 16:03:42.269][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.270][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.271][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-25 16:03:42.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-25 16:03:42.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.275][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-25 16:03:42.276][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-25 16:03:42.277][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.278][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.279][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-25 16:03:42.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-25 16:03:42.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.283][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-25 16:03:42.284][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-25 16:03:42.284][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.285][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.287][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-25 16:03:42.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-25 16:03:42.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.290][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-25 16:03:42.291][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-25 16:03:42.292][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.293][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.294][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-25 16:03:42.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-25 16:03:42.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.302][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-25 16:03:42.303][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-25 16:03:42.304][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.305][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.306][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-25 16:03:42.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-25 16:03:42.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.310][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-25 16:03:42.311][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-25 16:03:42.312][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.312][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.314][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-25 16:03:42.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-25 16:03:42.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.317][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-25 16:03:42.318][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:03:42.319][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.320][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.321][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-25 16:03:42.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:03:42.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.325][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-25 16:03:42.326][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-25 16:03:42.327][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.328][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.329][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-25 16:03:42.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-25 16:03:42.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.332][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:03:42.333][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:03:42.334][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.335][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.336][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:03:42.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:03:42.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.340][ef$get] Asked field names are: description.
biodb.TRACE[2025-01-25 16:03:42.341][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-01-25 16:03:42.342][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.343][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.344][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-25 16:03:42.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-25 16:03:42.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.347][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-25 16:03:42.348][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-25 16:03:42.349][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.350][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.351][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-25 16:03:42.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-25 16:03:42.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.355][ef$get] Asked field names are: super.class.
biodb.TRACE[2025-01-25 16:03:42.356][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-25 16:03:42.357][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.358][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.359][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2025-01-25 16:03:42.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-25 16:03:42.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.362][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:03:42.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:03:42.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.366][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:03:42.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:03:42.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.370][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:03:42.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:03:42.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.373][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-25 16:03:42.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-25 16:03:42.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.377][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-25 16:03:42.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-25 16:03:42.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.381][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-25 16:03:42.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-25 16:03:42.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.384][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-25 16:03:42.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-25 16:03:42.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.388][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-25 16:03:42.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-25 16:03:42.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.391][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-25 16:03:42.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-25 16:03:42.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.395][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-25 16:03:42.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-25 16:03:42.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.399][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-25 16:03:42.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-25 16:03:42.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.402][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-25 16:03:42.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-25 16:03:42.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.406][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-25 16:03:42.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-25 16:03:42.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.409][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-25 16:03:42.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-25 16:03:42.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.413][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-25 16:03:42.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-25 16:03:42.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.417][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-25 16:03:42.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-25 16:03:42.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.420][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-25 16:03:42.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-25 16:03:42.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.424][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-25 16:03:42.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-25 16:03:42.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.431][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-25 16:03:42.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-25 16:03:42.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.435][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-25 16:03:42.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-25 16:03:42.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.438][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-25 16:03:42.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-25 16:03:42.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.442][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-01-25 16:03:42.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-25 16:03:42.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.446][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-01-25 16:03:42.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-25 16:03:42.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.449][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-01-25 16:03:42.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-25 16:03:42.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.453][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-25 16:03:42.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-25 16:03:42.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.456][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-25 16:03:42.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-25 16:03:42.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.460][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-25 16:03:42.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-25 16:03:42.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.464][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-25 16:03:42.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-25 16:03:42.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.467][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-25 16:03:42.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-25 16:03:42.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.471][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-25 16:03:42.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-25 16:03:42.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.474][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-25 16:03:42.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-25 16:03:42.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.478][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-25 16:03:42.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-25 16:03:42.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.482][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-25 16:03:42.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-25 16:03:42.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.485][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-25 16:03:42.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:03:42.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.489][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-25 16:03:42.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:03:42.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.492][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-25 16:03:42.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:03:42.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.496][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-25 16:03:42.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-25 16:03:42.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.500][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-25 16:03:42.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-25 16:03:42.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.503][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-25 16:03:42.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-25 16:03:42.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.507][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-25 16:03:42.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-25 16:03:42.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.511][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-25 16:03:42.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-25 16:03:42.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.514][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-25 16:03:42.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-25 16:03:42.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.518][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:03:42.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:03:42.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.521][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:03:42.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:03:42.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.525][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:03:42.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:03:42.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.529][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-25 16:03:42.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-25 16:03:42.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.532][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-25 16:03:42.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-25 16:03:42.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.536][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-25 16:03:42.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-25 16:03:42.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.539][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-25 16:03:42.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-25 16:03:42.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.543][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-25 16:03:42.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-25 16:03:42.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.547][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-25 16:03:42.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-25 16:03:42.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.550][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-25 16:03:42.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-25 16:03:42.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.554][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-25 16:03:42.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-25 16:03:42.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.561][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-25 16:03:42.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-25 16:03:42.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.565][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-01-25 16:03:42.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:03:42.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.568][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-25 16:03:42.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:03:42.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.572][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-25 16:03:42.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:03:42.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.575][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-25 16:03:42.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:03:42.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.579][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-01-25 16:03:42.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:03:42.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.583][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:03:42.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:03:42.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.587][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:03:42.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:03:42.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.591][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:03:42.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:03:42.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.594][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:03:42.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:03:42.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.598][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:03:42.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:03:42.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.602][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-01-25 16:03:42.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-01-25 16:03:42.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.606][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-01-25 16:03:42.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-01-25 16:03:42.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.609][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:03:42.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:03:42.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.613][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-01-25 16:03:42.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-01-25 16:03:42.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.616][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:03:42.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:03:42.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.620][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:03:42.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:03:42.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.624][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:03:42.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:03:42.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.627][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:03:42.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:03:42.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.631][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:03:42.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:03:42.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.635][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:03:42.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:03:42.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-25 16:03:42.638][self$createEntryFromContent] Accession numbers: HMDB0000001.
biodb.TRACE[2025-01-25 16:03:42.639][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-01-25 16:03:42.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-01-25 16:03:42.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.643][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-01-25 16:03:42.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-01-25 16:03:42.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.646][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-01-25 16:03:42.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-01-25 16:03:42.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-01-25 16:03:42.656][biodb::testThat]
biodb.INFO [2025-01-25 16:03:42.657][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-01-25 16:03:42.658][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-25 16:03:42.659][biodb::testThat]
biodb.TRACE[2025-01-25 16:03:42.661][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:03:42.662][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:03:42.663][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.664][ef$get] fields variable is a list.
biodb.DEBUG[2025-01-25 16:03:42.665][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "name".
biodb.TRACE[2025-01-25 16:03:42.691][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:03:42.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:03:42.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.695][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:03:42.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:03:42.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.699][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:03:42.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:03:42.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-25 16:03:42.705][function(conn, opt)] With value "1-Methylhistidine".
biodb.DEBUG[2025-01-25 16:03:42.706][private$doSearchForEntries] fields NAMES = name
biodb.DEBUG[2025-01-25 16:03:42.707][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2025-01-25 16:03:42.707][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2025-01-25 16:03:42.709][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-25 16:03:42.710][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-25 16:03:42.712][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-01-25 16:03:42.713][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-25 16:03:42.714][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-01-25 16:03:42.715][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-01-25 16:03:42.716][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-01-25 16:03:42.717][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-01-25 16:03:42.718][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2025-01-25 16:03:42.719][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2025-01-25 16:03:42.719][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2025-01-25 16:03:42.721][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:03:42.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:03:42.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.725][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:03:42.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:03:42.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.728][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:03:42.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:03:42.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.732][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:03:42.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:03:42.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-25 16:03:42.736][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2025-01-25 16:03:42.736][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2025-01-25 16:03:42.737][function(conn, opt)] With found IDs [1]: "HMDB0000001".
biodb.TRACE[2025-01-25 16:03:42.747][ef$get] Asked field names are: description.
biodb.TRACE[2025-01-25 16:03:42.748][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-01-25 16:03:42.749][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.749][ef$get] fields variable is a list.
biodb.DEBUG[2025-01-25 16:03:42.750][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "description".
biodb.TRACE[2025-01-25 16:03:42.760][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-25 16:03:42.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-25 16:03:42.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.763][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-25 16:03:42.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-25 16:03:42.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.767][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-25 16:03:42.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-25 16:03:42.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-25 16:03:42.773][function(conn, opt)] With value "1-Methylhistidine, also known as 1-MHis, belongs to the class of organic compounds known as histidine and derivatives. Histidine and derivatives are compounds containing cysteine or a derivative thereof resulting from a reaction of cysteine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. 1-Methylhistidine is derived mainly from the anserine of dietary flesh sources, especially poultry. The enzyme, carnosinase, splits anserine into beta-alanine and 1-MHis. High levels of 1-MHis tend to inhibit the enzyme carnosinase and increase anserine levels. Conversely, genetic variants with deficient carnosinase activity in plasma show increased 1-MHis excretions when they consume a high meat diet. Reduced serum carnosinase activity is also found in patients with Parkinson's disease and multiple sclerosis and patients following a cerebrovascular accident. Vitamin E deficiency can lead to 1-methylhistidinuria from increased oxidative effects in skeletal muscle. 1-Methylhistidine is a biomarker for the consumption of meat, especially red meat.".
biodb.DEBUG[2025-01-25 16:03:42.825][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2025-01-25 16:03:42.826][private$doSearchForEntries] fields VALUES = 1-Methylhistidine, also known as 1-MHis, belongs to the class of organic compounds known as histidine and derivatives. Histidine and derivatives are compounds containing cysteine or a derivative thereof resulting from a reaction of cysteine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. 1-Methylhistidine is derived mainly from the anserine of dietary flesh sources, especially poultry. The enzyme, carnosinase, splits anserine into beta-alanine and 1-MHis. High levels of 1-MHis tend to inhibit the enzyme carnosinase and increase anserine levels. Conversely, genetic variants with deficient carnosinase activity in plasma show increased 1-MHis excretions when they consume a high meat diet. Reduced serum carnosinase activity is also found in patients with Parkinson's disease and multiple sclerosis and patients following a cerebrovascular accident. Vitamin E deficiency can lead to 1-methylhistidinuria from increased oxidative effects in skeletal muscle. 1-Methylhistidine is a biomarker for the consumption of meat, especially red meat.
biodb.DEBUG[2025-01-25 16:03:42.827][private$doSearchForEntries] fields VALUES = 1-Methylhistidine, also known as 1-MHis, belongs to the class of organic compounds known as histidine and derivatives. Histidine and derivatives are compounds containing cysteine or a derivative thereof resulting from a reaction of cysteine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. 1-Methylhistidine is derived mainly from the anserine of dietary flesh sources, especially poultry. The enzyme, carnosinase, splits anserine into beta-alanine and 1-MHis. High levels of 1-MHis tend to inhibit the enzyme carnosinase and increase anserine levels. Conversely, genetic variants with deficient carnosinase activity in plasma show increased 1-MHis excretions when they consume a high meat diet. Reduced serum carnosinase activity is also found in patients with Parkinson's disease and multiple sclerosis and patients following a cerebrovascular accident. Vitamin E deficiency can lead to 1-methylhistidinuria from increased oxidative effects in skeletal muscle. 1-Methylhistidine is a biomarker for the consumption of meat, especially red meat.
biodb.DEBUG[2025-01-25 16:03:42.840][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-25 16:03:42.841][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-25 16:03:42.842][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-01-25 16:03:42.844][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-25 16:03:42.844][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-01-25 16:03:42.858][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-01-25 16:03:42.859][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-01-25 16:03:42.860][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-01-25 16:03:42.861][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2025-01-25 16:03:42.862][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2025-01-25 16:03:42.863][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2025-01-25 16:03:42.864][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-25 16:03:42.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-25 16:03:42.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.868][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-25 16:03:42.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-25 16:03:42.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.872][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-25 16:03:42.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-25 16:03:42.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.875][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-25 16:03:42.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-25 16:03:42.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-25 16:03:42.879][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2025-01-25 16:03:42.880][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2025-01-25 16:03:42.881][function(conn, opt)] With found IDs [1]: "HMDB0000001".
biodb.TRACE[2025-01-25 16:03:42.890][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-25 16:03:42.891][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-25 16:03:42.892][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.893][ef$get] fields variable is a list.
biodb.DEBUG[2025-01-25 16:03:42.894][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "secondary.accessions".
biodb.TRACE[2025-01-25 16:03:42.904][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-25 16:03:42.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-25 16:03:42.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.907][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-25 16:03:42.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-25 16:03:42.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.911][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-25 16:03:42.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-25 16:03:42.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-25 16:03:42.916][function(conn, opt)] With value "HMDB00001".
biodb.DEBUG[2025-01-25 16:03:42.918][private$doSearchForEntries] fields NAMES = secondary.accessions
biodb.DEBUG[2025-01-25 16:03:42.919][private$doSearchForEntries] fields VALUES = HMDB00001
biodb.DEBUG[2025-01-25 16:03:42.919][private$doSearchForEntries] fields VALUES = HMDB00001
biodb.DEBUG[2025-01-25 16:03:42.921][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-25 16:03:42.922][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-25 16:03:42.927][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-01-25 16:03:42.928][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-25 16:03:42.929][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-01-25 16:03:42.930][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-01-25 16:03:42.931][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-01-25 16:03:42.932][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-01-25 16:03:42.933][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2025-01-25 16:03:42.934][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2025-01-25 16:03:42.935][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2025-01-25 16:03:42.936][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-25 16:03:42.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-25 16:03:42.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.940][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-25 16:03:42.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-25 16:03:42.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.944][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-25 16:03:42.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-25 16:03:42.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.947][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-25 16:03:42.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-25 16:03:42.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-25 16:03:42.951][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2025-01-25 16:03:42.952][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2025-01-25 16:03:42.953][function(conn, opt)] With found IDs [1]: "HMDB0000001".
biodb.INFO [2025-01-25 16:03:42.965][biodb::testThat]
biodb.INFO [2025-01-25 16:03:42.966][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-01-25 16:03:42.966][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-25 16:03:42.967][biodb::testThat]
biodb.TRACE[2025-01-25 16:03:42.976][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:03:42.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:03:42.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.980][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:03:42.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:03:42.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:42.983][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:03:42.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:03:42.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:42.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-25 16:03:42.996][private$doSearchForEntries] fields NAMES = name
biodb.DEBUG[2025-01-25 16:03:42.996][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2025-01-25 16:03:42.997][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2025-01-25 16:03:42.999][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-25 16:03:43.000][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-25 16:03:43.001][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-01-25 16:03:43.003][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-25 16:03:43.004][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-01-25 16:03:43.005][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-01-25 16:03:43.006][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-01-25 16:03:43.007][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-01-25 16:03:43.007][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2025-01-25 16:03:43.008][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2025-01-25 16:03:43.009][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2025-01-25 16:03:43.011][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:03:43.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:03:43.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:43.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:43.014][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:03:43.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:03:43.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:43.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:43.018][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:03:43.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:03:43.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:43.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:43.022][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:03:43.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:03:43.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:43.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-25 16:03:43.025][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2025-01-25 16:03:43.026][private$doSearchForEntries] COUNT IDS = 1
biodb.INFO [2025-01-25 16:03:43.038][biodb::testThat]
biodb.INFO [2025-01-25 16:03:43.039][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-01-25 16:03:43.040][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-25 16:03:43.041][biodb::testThat]
biodb.TRACE[2025-01-25 16:03:43.062][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-25 16:03:43.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-25 16:03:43.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:43.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:43.066][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-25 16:03:43.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-25 16:03:43.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:43.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:43.070][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-01-25 16:03:43.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-01-25 16:03:43.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:43.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:43.073][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-01-25 16:03:43.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-01-25 16:03:43.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:43.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:43.114][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-25 16:03:43.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-25 16:03:43.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:43.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:43.118][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-25 16:03:43.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-25 16:03:43.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:43.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:43.122][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-01-25 16:03:43.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-01-25 16:03:43.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:43.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:43.125][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-01-25 16:03:43.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-01-25 16:03:43.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:43.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-01-25 16:03:43.134][biodb::testThat]
biodb.INFO [2025-01-25 16:03:43.135][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-01-25 16:03:43.136][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-25 16:03:43.136][biodb::testThat]
biodb.INFO [2025-01-25 16:03:43.143][biodb::testThat]
biodb.INFO [2025-01-25 16:03:43.144][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-01-25 16:03:43.145][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-25 16:03:43.146][biodb::testThat]
biodb.INFO [2025-01-25 16:03:43.152][biodb::testThat]
biodb.INFO [2025-01-25 16:03:43.153][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-01-25 16:03:43.154][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-25 16:03:43.155][biodb::testThat]
biodb.DEBUG[2025-01-25 16:03:43.158][function(conn, opt)] Trying to download "http://www.hmdb.ca/metabolites/HMDB0000001".
biodb.DEBUG[2025-01-25 16:03:54.578][getUrlContent] Use RCurl for downloading content of URL http://www.hmdb.ca/metabolites/HMDB0000001.
biodb.INFO [2025-01-25 16:03:54.662][biodb::testThat]
biodb.INFO [2025-01-25 16:03:54.665][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-01-25 16:03:54.667][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-25 16:03:54.669][biodb::testThat]
biodb.DEBUG[2025-01-25 16:03:56.110][getUrlContent] Use RCurl for downloading content of URL http://www.hmdb.ca/structures/HMDB0000001/image.png.
biodb.TRACE[2025-01-25 16:03:56.139][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:03:56.140][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:03:56.141][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:56.142][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:56.143][ef$get] Asked field names are: description.
biodb.TRACE[2025-01-25 16:03:56.144][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-01-25 16:03:56.145][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:56.146][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:56.156][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-25 16:03:56.160][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-25 16:03:56.161][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:56.162][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:56.163][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:03:56.164][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:03:56.165][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:56.166][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:56.167][ef$get] Asked field names are: description.
biodb.TRACE[2025-01-25 16:03:56.168][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-01-25 16:03:56.169][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:56.170][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:56.170][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-25 16:03:56.172][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-25 16:03:56.172][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:56.173][ef$get] fields variable is a list.
biodb.INFO [2025-01-25 16:03:56.174][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-01-25 16:03:56.176][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler
biodb.INFO [2025-01-25 16:03:56.177][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2025-01-25 16:03:56.178][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-01-25 16:03:56.178][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:03:56.179][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:03:56.180][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:56.181][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 16:03:56.182][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:56.183][FUN] Functions in observer 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 0 | WARN 0 | SKIP 0 | PASS 147 ]
> 
> proc.time()
   user  system elapsed 
  4.749   0.191  17.600

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-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_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc-longtests/meat/biodbHmdb.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* 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 ‘1.12.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbHmdb’ can be installed ... WARNING
Found the following significant warnings:
  EntryMaker.hpp:23:21: warning: ‘EntryMaker::accession_tag’ will be initialized after [-Wreorder]
  EntryMaker.hpp:22:14: warning:   ‘bool EntryMaker::closed’ [-Wreorder]
  EntryMaker.cpp:5:1: warning:   when initialized here [-Wreorder]
See ‘/home/biocbuild/bbs-3.20-bioc-longtests/meat/biodbHmdb.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking installed package size ... NOTE
  installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
* 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’
 OK
* DONE

Status: 2 WARNINGs, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc-longtests/meat/biodbHmdb.Rcheck/00check.log’
for details.

Installation output

biodbHmdb.Rcheck/00install.out

* installing *source* package ‘biodbHmdb’ ...
** 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-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c EntryMaker.cpp -o EntryMaker.o
In file included from EntryMaker.cpp:1:
EntryMaker.hpp: In constructor ‘EntryMaker::EntryMaker()’:
EntryMaker.hpp:23:21: warning: ‘EntryMaker::accession_tag’ will be initialized after [-Wreorder]
   23 |         TagDetector accession_tag;
      |                     ^~~~~~~~~~~~~
EntryMaker.hpp:22:14: warning:   ‘bool EntryMaker::closed’ [-Wreorder]
   22 |         bool closed;
      |              ^~~~~~
EntryMaker.cpp:5:1: warning:   when initialized here [-Wreorder]
    5 | EntryMaker::EntryMaker() :
      | ^~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c FileEntryMaker.cpp -o FileEntryMaker.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c StringEnrtryMaker.cpp -o StringEnrtryMaker.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c TagDetector.cpp -o TagDetector.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c XmlSplitter.cpp -o XmlSplitter.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c extractXmlEntries.cpp -o extractXmlEntries.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c test-100-TagDetector.cpp -o test-100-TagDetector.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c test-150-StringEntryMaker.cpp -o test-150-StringEntryMaker.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c test-200-XmlSplitter.cpp -o test-200-XmlSplitter.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c test-runner.cpp -o test-runner.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.20-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-3.20-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.20-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)