Back to Long Tests report for BioC 3.20

This page was generated on 2025-01-18 23:55 -0500 (Sat, 18 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" 4489
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: 2025-01-18 09:55 -0500 (Sat, 18 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  ERROR  
merida1macOS 12.7.5 Monterey / x86_64  ERROR  

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: 2025-01-18 16:02:34 -0500 (Sat, 18 Jan 2025)
EndedAt: 2025-01-18 16:03:58 -0500 (Sat, 18 Jan 2025)
EllapsedTime: 84.0 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

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

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

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

> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbHmdb)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbHmdb")
biodb.INFO [2025-01-18 16:03:34.253][biodb::testContext]
biodb.INFO [2025-01-18 16:03:34.255][biodb::testContext] ********************************************************************************
biodb.INFO [2025-01-18 16:03:34.256][biodb::testContext] Test context - Generic long tests
biodb.INFO [2025-01-18 16:03:34.256][biodb::testContext] ********************************************************************************
biodb.INFO [2025-01-18 16:03:34.257][biodb::testContext]
biodb.INFO [2025-01-18 16:03:34.263][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2025-01-18 16:03:34.264][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-01-18 16:03:34.271][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-18 16:03:34.272][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-01-18 16:03:34.273][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-01-18 16:03:34.273][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:03:34.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:03:34.275][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:03:34.276][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-01-18 16:03:34.292][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-01-18 16:03:34.293][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:03:34.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:03:34.294][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:03:34.295][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-01-18 16:03:34.296][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-01-18 16:03:34.297][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:03:34.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:03:34.299][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:03:34.299][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-01-18 16:03:34.300][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-01-18 16:03:34.301][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-01-18 16:03:34.302][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:03:34.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:03:34.304][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:03:34.304][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-01-18 16:03:34.305][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-01-18 16:03:34.306][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-01-18 16:03:34.307][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:03:34.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:03:34.309][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:03:34.309][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-01-18 16:03:34.310][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-01-18 16:03:34.311][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:03:34.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:03:34.313][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[2025-01-18 16:03:34.313][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-01-18 16:03:34.314][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-01-18 16:03:34.315][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-01-18 16:03:34.316][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:03:34.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:03:34.318][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:03:34.318][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-01-18 16:03:34.319][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-01-18 16:03:34.320][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:03:34.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:03:34.322][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:03:34.323][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-01-18 16:03:34.323][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-01-18 16:03:34.324][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-01-18 16:03:34.325][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:03:34.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:03:34.327][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:03:34.327][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-01-18 16:03:34.328][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-01-18 16:03:34.329][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-01-18 16:03:34.330][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-01-18 16:03:34.331][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-01-18 16:03:34.332][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-01-18 16:03:34.333][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:03:34.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:03:34.334][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:03:34.335][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-01-18 16:03:34.336][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-01-18 16:03:34.337][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:03:34.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:03:34.338][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:03:34.339][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-01-18 16:03:34.340][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-01-18 16:03:34.341][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:03:34.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:03:34.342][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:03:34.343][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-01-18 16:03:34.344][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-01-18 16:03:34.345][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:03:34.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:03:34.347][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:03:34.347][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-01-18 16:03:34.348][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-01-18 16:03:34.349][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:03:34.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:03:34.351][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:03:34.351][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-01-18 16:03:34.352][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-01-18 16:03:34.353][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:03:34.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:03:34.355][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:03:34.356][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-01-18 16:03:34.356][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-01-18 16:03:34.361][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-01-18 16:03:34.362][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:03:34.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:03:34.364][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:03:34.365][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-01-18 16:03:34.366][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-01-18 16:03:34.366][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-01-18 16:03:34.367][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:03:34.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:03:34.369][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:03:34.372][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-01-18 16:03:34.401][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-18 16:03:34.422][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-01-18 16:03:34.423][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-18 16:03:34.424][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-18 16:03:34.425][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-18 16:03:34.425][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-18 16:03:34.426][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-18 16:03:34.427][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-18 16:03:34.428][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-01-18 16:03:34.429][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-18 16:03:34.430][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-18 16:03:34.431][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-01-18 16:03:34.432][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-18 16:03:34.432][self$setPropertyValue]
biodb.DEBUG[2025-01-18 16:03:34.433][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-18 16:03:34.434][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-18 16:03:34.434][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-01-18 16:03:34.434][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-01-18 16:03:34.434][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-01-18 16:03:34.434][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-01-18 16:03:34.435][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-18 16:03:34.436][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-18 16:03:34.437][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-18 16:03:34.438][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-18 16:03:34.438][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-18 16:03:34.439][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-18 16:03:34.440][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-18 16:03:34.441][self$setPropertyValue]
biodb.DEBUG[2025-01-18 16:03:34.442][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-18 16:03:34.443][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-18 16:03:34.444][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-18 16:03:34.444][self$setPropertyValue]
biodb.DEBUG[2025-01-18 16:03:34.446][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-01-18 16:03:34.447][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-18 16:03:34.448][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-01-18 16:03:34.449][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-18 16:03:34.450][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-18 16:03:34.451][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-18 16:03:34.451][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-18 16:03:34.452][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-18 16:03:34.453][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-18 16:03:34.454][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-01-18 16:03:34.455][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-18 16:03:34.456][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-18 16:03:34.457][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-01-18 16:03:34.458][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-18 16:03:34.458][self$setPropertyValue]
biodb.DEBUG[2025-01-18 16:03:34.459][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-18 16:03:34.460][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-18 16:03:34.460][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-01-18 16:03:34.460][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-01-18 16:03:34.460][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-01-18 16:03:34.460][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-01-18 16:03:34.461][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-18 16:03:34.462][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-18 16:03:34.463][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-18 16:03:34.464][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-18 16:03:34.464][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-18 16:03:34.465][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-18 16:03:34.466][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-18 16:03:34.467][self$setPropertyValue]
biodb.DEBUG[2025-01-18 16:03:34.468][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-18 16:03:34.469][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-18 16:03:34.469][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-18 16:03:34.470][self$setPropertyValue]
biodb.DEBUG[2025-01-18 16:03:34.471][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-01-18 16:03:34.473][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-01-18 16:03:34.474][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-01-18 16:03:34.475][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-18 16:03:34.476][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-18 16:03:34.476][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-18 16:03:34.477][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-18 16:03:34.478][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-18 16:03:34.479][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-18 16:03:34.480][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-01-18 16:03:34.481][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-18 16:03:34.482][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-01-18 16:03:34.483][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-01-18 16:03:34.483][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-18 16:03:34.484][self$setPropertyValue]
biodb.DEBUG[2025-01-18 16:03:34.485][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-18 16:03:34.486][self$setPropertyValue]
biodb.DEBUG[2025-01-18 16:03:34.487][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-18 16:03:34.488][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-18 16:03:34.488][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-18 16:03:34.489][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-18 16:03:34.490][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-18 16:03:34.491][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-18 16:03:34.492][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-18 16:03:34.493][self$setPropertyValue]
biodb.DEBUG[2025-01-18 16:03:34.493][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-18 16:03:34.494][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-18 16:03:34.495][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-18 16:03:34.496][self$setPropertyValue]
biodb.DEBUG[2025-01-18 16:03:34.497][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-01-18 16:03:34.499][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-01-18 16:03:34.499][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-01-18 16:03:34.500][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-18 16:03:34.501][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-18 16:03:34.502][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-18 16:03:34.503][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-18 16:03:34.504][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-18 16:03:34.505][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-18 16:03:34.506][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-01-18 16:03:34.506][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-18 16:03:34.507][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-01-18 16:03:34.508][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-01-18 16:03:34.509][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-18 16:03:34.510][self$setPropertyValue]
biodb.DEBUG[2025-01-18 16:03:34.511][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-18 16:03:34.512][self$setPropertyValue]
biodb.DEBUG[2025-01-18 16:03:34.513][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-18 16:03:34.513][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-18 16:03:34.514][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-18 16:03:34.515][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-18 16:03:34.516][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-18 16:03:34.517][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-18 16:03:34.517][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-18 16:03:34.518][self$setPropertyValue]
biodb.DEBUG[2025-01-18 16:03:34.519][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-18 16:03:34.520][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-18 16:03:34.521][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-18 16:03:34.522][self$setPropertyValue]
biodb.DEBUG[2025-01-18 16:03:34.525][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-18 16:03:34.526][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:03:34.527][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:03:34.527][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:03:34.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:03:34.529][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:03:34.530][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:03:34.531][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[2025-01-18 16:03:34.531][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:03:34.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:03:34.533][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:03:34.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:03:34.535][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[2025-01-18 16:03:34.535][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:03:34.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:03:34.537][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:03:34.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:03:34.538][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:03:34.539][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:03:34.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:03:34.541][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:03:34.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:03:34.542][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:03:34.543][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:03:34.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:03:34.545][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:03:34.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:03:34.546][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:03:34.547][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:03:34.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:03:34.549][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:03:34.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:03:34.550][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:03:34.551][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:03:34.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:03:34.552][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:03:34.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:03:34.554][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:03:34.555][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:03:34.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:03:34.556][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:03:34.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:03:34.558][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:03:34.559][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:03:34.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:03:34.560][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:03:34.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:03:34.562][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:03:34.563][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:03:34.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:03:34.564][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:03:34.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:03:34.566][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:03:34.567][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:03:34.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:03:34.568][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:03:34.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:03:34.570][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:03:34.570][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:03:34.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:03:34.572][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:03:34.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:03:34.574][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:03:34.574][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:03:34.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:03:34.580][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:03:34.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:03:34.581][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:03:34.582][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:03:34.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:03:34.584][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:03:34.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:03:34.585][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:03:34.586][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:03:34.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:03:34.588][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:03:34.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:03:34.589][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:03:34.590][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:03:34.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:03:34.591][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:03:34.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:03:34.593][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:03:34.594][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:03:34.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:03:34.595][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:03:34.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:03:34.597][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:03:34.598][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-01-18 16:03:34.602][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-01-18 16:03:34.603][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-01-18 16:03:34.604][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-01-18 16:03:34.606][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-01-18 16:03:34.607][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-01-18 16:03:34.608][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-01-18 16:03:34.609][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-01-18 16:03:34.611][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-01-18 16:03:34.612][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-01-18 16:03:34.613][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-01-18 16:03:34.614][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-01-18 16:03:34.616][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-01-18 16:03:34.617][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-01-18 16:03:34.618][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-01-18 16:03:34.619][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-01-18 16:03:34.621][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-01-18 16:03:34.622][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-01-18 16:03:34.623][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-01-18 16:03:34.624][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-01-18 16:03:34.626][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-01-18 16:03:34.627][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-01-18 16:03:34.628][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-01-18 16:03:34.629][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-01-18 16:03:34.631][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-01-18 16:03:34.632][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-01-18 16:03:34.633][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-01-18 16:03:34.634][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-01-18 16:03:34.635][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-01-18 16:03:34.637][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-01-18 16:03:34.638][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-01-18 16:03:34.639][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-01-18 16:03:34.640][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-01-18 16:03:34.642][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-01-18 16:03:34.643][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-01-18 16:03:34.644][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-01-18 16:03:34.645][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-01-18 16:03:34.647][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-01-18 16:03:34.648][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-01-18 16:03:34.649][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-01-18 16:03:34.650][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-01-18 16:03:34.652][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-01-18 16:03:34.653][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-01-18 16:03:34.654][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-01-18 16:03:34.655][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-01-18 16:03:34.657][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-01-18 16:03:34.658][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-01-18 16:03:34.659][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-01-18 16:03:34.660][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-01-18 16:03:34.661][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-01-18 16:03:34.663][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-01-18 16:03:34.664][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-01-18 16:03:34.665][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-01-18 16:03:34.666][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-01-18 16:03:34.668][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-01-18 16:03:34.669][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-01-18 16:03:34.670][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-01-18 16:03:34.671][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-01-18 16:03:34.673][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-01-18 16:03:34.674][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-01-18 16:03:34.675][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-01-18 16:03:34.676][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-01-18 16:03:34.677][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-01-18 16:03:34.679][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-01-18 16:03:34.680][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-01-18 16:03:34.681][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-01-18 16:03:34.682][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-01-18 16:03:34.691][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-01-18 16:03:34.694][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-01-18 16:03:34.695][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-01-18 16:03:34.697][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-01-18 16:03:34.698][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-01-18 16:03:34.699][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-01-18 16:03:34.701][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-01-18 16:03:34.702][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-01-18 16:03:34.704][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-01-18 16:03:34.705][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-01-18 16:03:34.707][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-01-18 16:03:34.708][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-01-18 16:03:34.709][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-01-18 16:03:34.711][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-01-18 16:03:34.712][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-01-18 16:03:34.714][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-01-18 16:03:34.721][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-01-18 16:03:34.724][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2025-01-18 16:03:34.727][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-18 16:03:34.728][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:03:34.729][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:03:34.730][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:03:34.731][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[2025-01-18 16:03:34.736][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:03:34.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-18 16:03:34.737][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-18 16:03:34.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:03:34.739][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:03:34.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:03:34.741][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:03:34.742][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:03:34.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-18 16:03:34.743][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-18 16:03:34.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:03:34.745][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:03:34.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:03:34.747][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:03:34.748][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:03:34.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-18 16:03:34.750][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-18 16:03:34.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:03:34.751][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:03:34.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:03:34.753][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:03:34.754][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:03:34.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-18 16:03:34.773][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-18 16:03:34.774][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:03:34.775][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:03:34.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:03:34.776][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:03:34.777][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:03:34.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-18 16:03:34.779][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-18 16:03:34.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:03:34.781][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:03:34.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:03:34.782][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:03:34.783][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:03:34.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-18 16:03:34.785][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-18 16:03:34.786][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:03:34.787][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:03:34.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:03:34.788][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:03:34.789][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:03:34.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-18 16:03:34.791][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-18 16:03:34.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:03:34.793][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:03:34.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:03:34.795][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:03:34.795][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:03:34.796][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-18 16:03:34.797][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-18 16:03:34.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:03:34.799][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:03:34.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:03:34.801][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:03:34.802][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:03:34.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-18 16:03:34.804][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-18 16:03:34.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:03:34.806][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:03:34.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:03:34.807][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:03:34.808][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:03:34.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-18 16:03:34.810][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-18 16:03:34.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:03:34.811][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:03:34.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:03:34.813][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:03:34.814][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:03:34.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-18 16:03:34.816][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-18 16:03:34.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:03:34.817][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:03:34.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:03:34.819][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:03:34.820][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:03:34.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-18 16:03:34.822][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-18 16:03:34.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:03:34.823][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:03:34.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:03:34.825][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:03:34.826][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:03:34.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-18 16:03:34.828][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-18 16:03:34.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:03:34.829][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:03:34.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:03:34.831][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:03:34.832][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:03:34.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-18 16:03:34.834][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-18 16:03:34.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:03:34.835][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:03:34.836][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:03:34.837][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:03:34.838][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:03:34.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-18 16:03:34.840][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-18 16:03:34.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:03:34.841][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:03:34.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:03:34.843][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:03:34.844][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:03:34.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-18 16:03:34.845][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-18 16:03:34.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:03:34.847][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:03:34.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:03:34.849][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:03:34.850][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:03:34.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-18 16:03:34.851][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-18 16:03:34.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:03:34.853][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:03:34.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:03:34.855][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:03:34.856][biodb$getConfig()$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-01-18 16:03:34.857][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-18 16:03:34.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-18 16:03:34.858][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-18 16:03:34.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:03:34.860][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:03:34.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:03:34.862][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-18 16:03:34.863][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/definitions.yml".
biodb.DEBUG[2025-01-18 16:03:34.873][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2025-01-18 16:03:34.874][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-18 16:03:34.875][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-01-18 16:03:34.876][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-18 16:03:34.877][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-18 16:03:34.878][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-01-18 16:03:34.879][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2025-01-18 16:03:34.880][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-01-18 16:03:34.881][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-18 16:03:34.882][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-01-18 16:03:34.883][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-18 16:03:34.884][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-18 16:03:34.885][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2025-01-18 16:03:34.886][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-18 16:03:34.887][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2025-01-18 16:03:34.887][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2025-01-18 16:03:34.887][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2025-01-18 16:03:34.887][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2025-01-18 16:03:34.887][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2025-01-18 16:03:34.887][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2025-01-18 16:03:34.887][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2025-01-18 16:03:34.887][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2025-01-18 16:03:34.887][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2025-01-18 16:03:34.887][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2025-01-18 16:03:34.887][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2025-01-18 16:03:34.887][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2025-01-18 16:03:34.887][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2025-01-18 16:03:34.887][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2025-01-18 16:03:34.887][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2025-01-18 16:03:34.887][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2025-01-18 16:03:34.887][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2025-01-18 16:03:34.887][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2025-01-18 16:03:34.888][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-01-18 16:03:34.888][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-18 16:03:34.888][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2025-01-18 16:03:34.888][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2025-01-18 16:03:34.889][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-01-18 16:03:34.890][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-18 16:03:34.891][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-18 16:03:34.892][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-18 16:03:34.893][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-18 16:03:34.893][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-18 16:03:34.894][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-18 16:03:34.895][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2025-01-18 16:03:34.895][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2025-01-18 16:03:34.896][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-18 16:03:34.897][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-18 16:03:34.898][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-01-18 16:03:34.899][self$setPropertyValue]
biodb.DEBUG[2025-01-18 16:03:34.904][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2025-01-18 16:03:34.905][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-01-18 16:03:34.907][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-01-18 16:03:34.908][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-01-18 16:03:34.909][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-01-18 16:03:34.930][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2025-01-18 16:03:34.931][initialize] Register connector hmdb.metabolites with the request scheduler
biodb.DEBUG[2025-01-18 16:03:34.935][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites.
biodb.DEBUG[2025-01-18 16:03:34.938][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2025-01-18 16:03:34.942][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-01-18 16:03:34.943][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-01-18 16:03:34.944][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca".
biodb.DEBUG[2025-01-18 16:03:34.945][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.INFO [2025-01-18 16:03:34.981][biodb::testThat]
biodb.INFO [2025-01-18 16:03:34.982][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-01-18 16:03:34.983][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-18 16:03:34.983][biodb::testThat]
biodb.TRACE[2025-01-18 16:03:34.987][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[2025-01-18 16:03:34.988][biodb$getFactory()$createEntryFromCo ...] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-01-18 16:03:34.991][biodb$getFactory()$createEntryFromCo ...] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-01-18 16:03:34.998][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-18 16:03:34.999][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-18 16:03:35.000][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-18 16:03:35.011][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:03:35.012][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:03:35.013][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:03:35.013][FUN] Functions in observer BiodbConfig: [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[2025-01-18 16:03:35.023][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-18 16:03:35.024][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-18 16:03:35.025][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.026][ef$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.028][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-18 16:03:35.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-18 16:03:35.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.042][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-18 16:03:35.043][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-18 16:03:35.044][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.044][ef$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.068][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-18 16:03:35.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-18 16:03:35.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.071][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-18 16:03:35.072][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-18 16:03:35.073][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.074][ef$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.075][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-18 16:03:35.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-18 16:03:35.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.079][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-18 16:03:35.080][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-18 16:03:35.081][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.082][ef$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.083][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-18 16:03:35.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-18 16:03:35.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.086][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-18 16:03:35.087][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-18 16:03:35.088][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.089][ef$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.090][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-18 16:03:35.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-18 16:03:35.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.094][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-18 16:03:35.095][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-18 16:03:35.095][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.096][ef$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.097][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-18 16:03:35.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-18 16:03:35.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.101][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-18 16:03:35.102][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-18 16:03:35.103][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.104][ef$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.105][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-18 16:03:35.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-18 16:03:35.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.108][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-18 16:03:35.109][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-18 16:03:35.110][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.111][ef$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.112][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-18 16:03:35.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-18 16:03:35.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.116][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-18 16:03:35.117][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-18 16:03:35.118][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.118][ef$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.120][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-18 16:03:35.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-18 16:03:35.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.129][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-18 16:03:35.130][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-18 16:03:35.131][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.132][ef$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.133][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-18 16:03:35.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-18 16:03:35.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.137][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-18 16:03:35.137][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-18 16:03:35.138][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.139][ef$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.140][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-18 16:03:35.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-18 16:03:35.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.144][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-18 16:03:35.145][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-18 16:03:35.146][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.146][ef$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.148][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-18 16:03:35.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-18 16:03:35.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.151][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-18 16:03:35.152][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-18 16:03:35.153][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.154][ef$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.155][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-18 16:03:35.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-18 16:03:35.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.158][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-18 16:03:35.159][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-18 16:03:35.160][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.161][ef$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.162][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-18 16:03:35.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-18 16:03:35.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.166][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-18 16:03:35.167][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-18 16:03:35.167][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.168][ef$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.169][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-18 16:03:35.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-18 16:03:35.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.173][ef$get] Asked field names are: description.
biodb.TRACE[2025-01-18 16:03:35.174][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-01-18 16:03:35.175][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.176][ef$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.177][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-18 16:03:35.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-18 16:03:35.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.180][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-18 16:03:35.181][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-18 16:03:35.182][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.183][ef$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.184][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-18 16:03:35.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-18 16:03:35.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.187][ef$get] Asked field names are: super.class.
biodb.TRACE[2025-01-18 16:03:35.188][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-18 16:03:35.189][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.190][ef$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.191][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2025-01-18 16:03:35.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-18 16:03:35.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.195][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-18 16:03:35.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-18 16:03:35.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.198][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-18 16:03:35.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-18 16:03:35.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.202][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-18 16:03:35.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-18 16:03:35.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.235][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-18 16:03:35.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-18 16:03:35.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.238][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-18 16:03:35.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-18 16:03:35.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.242][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-18 16:03:35.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-18 16:03:35.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.245][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-18 16:03:35.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-18 16:03:35.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.249][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-18 16:03:35.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-18 16:03:35.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.255][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-18 16:03:35.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-18 16:03:35.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.259][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-18 16:03:35.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-18 16:03:35.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.262][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-18 16:03:35.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-18 16:03:35.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.266][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-18 16:03:35.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-18 16:03:35.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.269][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-18 16:03:35.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-18 16:03:35.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.273][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-18 16:03:35.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-18 16:03:35.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.277][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-18 16:03:35.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-18 16:03:35.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.280][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-18 16:03:35.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-18 16:03:35.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.284][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-18 16:03:35.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-18 16:03:35.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.287][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-18 16:03:35.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-18 16:03:35.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.291][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-18 16:03:35.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-18 16:03:35.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.294][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-18 16:03:35.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-18 16:03:35.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.298][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-18 16:03:35.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-18 16:03:35.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.301][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-01-18 16:03:35.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-18 16:03:35.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.305][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-01-18 16:03:35.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-18 16:03:35.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.308][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-01-18 16:03:35.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-18 16:03:35.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.312][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-18 16:03:35.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-18 16:03:35.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.315][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-18 16:03:35.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-18 16:03:35.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.319][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-18 16:03:35.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-18 16:03:35.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.322][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-18 16:03:35.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-18 16:03:35.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.326][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-18 16:03:35.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-18 16:03:35.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.329][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-18 16:03:35.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-18 16:03:35.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.333][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-18 16:03:35.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-18 16:03:35.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.336][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-18 16:03:35.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-18 16:03:35.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.340][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-18 16:03:35.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-18 16:03:35.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.343][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-18 16:03:35.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-18 16:03:35.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.347][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-18 16:03:35.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-18 16:03:35.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.350][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-18 16:03:35.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-18 16:03:35.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.354][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-18 16:03:35.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-18 16:03:35.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.357][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-18 16:03:35.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-18 16:03:35.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.361][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-18 16:03:35.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-18 16:03:35.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.365][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-18 16:03:35.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-18 16:03:35.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.368][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-18 16:03:35.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-18 16:03:35.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.372][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-18 16:03:35.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-18 16:03:35.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.375][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-18 16:03:35.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-18 16:03:35.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.379][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-18 16:03:35.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-18 16:03:35.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.382][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-18 16:03:35.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-18 16:03:35.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.389][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-18 16:03:35.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-18 16:03:35.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.392][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-18 16:03:35.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-18 16:03:35.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.396][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-18 16:03:35.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-18 16:03:35.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.399][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-18 16:03:35.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-18 16:03:35.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.403][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-18 16:03:35.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-18 16:03:35.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.406][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-18 16:03:35.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-18 16:03:35.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.410][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-18 16:03:35.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-18 16:03:35.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.414][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-18 16:03:35.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-18 16:03:35.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.417][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-18 16:03:35.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-18 16:03:35.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.421][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-01-18 16:03:35.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-18 16:03:35.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.424][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-18 16:03:35.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-18 16:03:35.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.428][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-18 16:03:35.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-18 16:03:35.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.431][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-18 16:03:35.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-18 16:03:35.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.435][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-01-18 16:03:35.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-18 16:03:35.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.454][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-18 16:03:35.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-18 16:03:35.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.458][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-18 16:03:35.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-18 16:03:35.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.461][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-18 16:03:35.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-18 16:03:35.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.465][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-18 16:03:35.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-18 16:03:35.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.468][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-18 16:03:35.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-18 16:03:35.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.472][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-01-18 16:03:35.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-01-18 16:03:35.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.475][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-01-18 16:03:35.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-01-18 16:03:35.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.479][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-18 16:03:35.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-18 16:03:35.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.482][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-01-18 16:03:35.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-01-18 16:03:35.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.486][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-18 16:03:35.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-18 16:03:35.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.489][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-18 16:03:35.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-18 16:03:35.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.493][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-18 16:03:35.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-18 16:03:35.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.497][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-18 16:03:35.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-18 16:03:35.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.500][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-18 16:03:35.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-18 16:03:35.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.503][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-18 16:03:35.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-18 16:03:35.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-18 16:03:35.507][biodb$getFactory()$createEntryFromCo ...] Accession numbers: HMDB0000001.
biodb.TRACE[2025-01-18 16:03:35.509][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-18 16:03:35.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-18 16:03:35.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.513][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-18 16:03:35.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-18 16:03:35.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.520][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-01-18 16:03:35.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-01-18 16:03:35.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.523][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-01-18 16:03:35.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-01-18 16:03:35.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.540][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-18 16:03:35.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-18 16:03:35.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.554][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-01-18 16:03:35.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-01-18 16:03:35.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.561][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-18 16:03:35.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-18 16:03:35.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.565][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-18 16:03:35.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-18 16:03:35.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.568][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-18 16:03:35.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-18 16:03:35.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.573][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-18 16:03:35.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-18 16:03:35.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.576][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-18 16:03:35.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-18 16:03:35.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.580][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-18 16:03:35.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-18 16:03:35.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.584][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-01-18 16:03:35.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-01-18 16:03:35.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.587][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-01-18 16:03:35.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-01-18 16:03:35.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.591][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-01-18 16:03:35.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-01-18 16:03:35.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.600][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-18 16:03:35.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-18 16:03:35.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.603][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-18 16:03:35.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-18 16:03:35.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.607][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-18 16:03:35.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-18 16:03:35.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.610][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-18 16:03:35.611][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-18 16:03:35.612][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.613][ef$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.614][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-18 16:03:35.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-18 16:03:35.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.624][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-18 16:03:35.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-18 16:03:35.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.627][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-18 16:03:35.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-18 16:03:35.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.631][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-18 16:03:35.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-18 16:03:35.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.634][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-18 16:03:35.635][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-18 16:03:35.636][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.637][ef$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.638][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-18 16:03:35.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-18 16:03:35.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.647][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-18 16:03:35.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-18 16:03:35.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.655][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-18 16:03:35.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-18 16:03:35.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.659][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-18 16:03:35.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-18 16:03:35.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.662][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-18 16:03:35.663][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-18 16:03:35.664][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.665][ef$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.666][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-18 16:03:35.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-18 16:03:35.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.675][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-18 16:03:35.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-18 16:03:35.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.679][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-18 16:03:35.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-18 16:03:35.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.682][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-18 16:03:35.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-18 16:03:35.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.686][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-18 16:03:35.687][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-18 16:03:35.688][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.688][ef$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.689][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-18 16:03:35.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-18 16:03:35.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.699][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-18 16:03:35.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-18 16:03:35.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.702][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-18 16:03:35.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-18 16:03:35.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.706][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-18 16:03:35.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-18 16:03:35.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.709][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-18 16:03:35.710][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-18 16:03:35.711][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.712][ef$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.713][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-18 16:03:35.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-18 16:03:35.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.723][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-18 16:03:35.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-18 16:03:35.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.726][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-18 16:03:35.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-18 16:03:35.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.730][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-18 16:03:35.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-18 16:03:35.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.733][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-18 16:03:35.734][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-18 16:03:35.735][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.736][ef$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.737][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-18 16:03:35.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-18 16:03:35.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.746][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-18 16:03:35.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-18 16:03:35.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.750][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-18 16:03:35.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-18 16:03:35.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.753][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-18 16:03:35.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-18 16:03:35.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.757][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-18 16:03:35.758][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-18 16:03:35.758][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.759][ef$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.760][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-18 16:03:35.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-18 16:03:35.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.770][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-18 16:03:35.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-18 16:03:35.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.773][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-18 16:03:35.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-18 16:03:35.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.777][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-18 16:03:35.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-18 16:03:35.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.784][ef$get] Asked field names are: description.
biodb.TRACE[2025-01-18 16:03:35.785][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-01-18 16:03:35.786][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.786][ef$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.787][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-18 16:03:35.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-18 16:03:35.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.797][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-18 16:03:35.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-18 16:03:35.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.801][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-18 16:03:35.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-18 16:03:35.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.804][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-18 16:03:35.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-18 16:03:35.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.808][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-18 16:03:35.809][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-18 16:03:35.809][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.810][ef$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.811][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-18 16:03:35.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-18 16:03:35.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.821][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-18 16:03:35.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-18 16:03:35.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.824][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-18 16:03:35.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-18 16:03:35.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.828][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-18 16:03:35.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-18 16:03:35.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.831][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-18 16:03:35.832][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-18 16:03:35.833][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.834][ef$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.835][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-18 16:03:35.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-18 16:03:35.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.845][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-18 16:03:35.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-18 16:03:35.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.848][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-18 16:03:35.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-18 16:03:35.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.852][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-18 16:03:35.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-18 16:03:35.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.855][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-18 16:03:35.856][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-18 16:03:35.857][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.858][ef$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.859][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-18 16:03:35.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-18 16:03:35.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.869][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-01-18 16:03:35.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-18 16:03:35.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.872][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-01-18 16:03:35.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-18 16:03:35.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.876][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-01-18 16:03:35.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-18 16:03:35.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.879][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-01-18 16:03:35.880][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-18 16:03:35.881][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.882][ef$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.883][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-01-18 16:03:35.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-18 16:03:35.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.893][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-18 16:03:35.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-18 16:03:35.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.896][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-18 16:03:35.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-18 16:03:35.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.900][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-18 16:03:35.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-18 16:03:35.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.903][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-18 16:03:35.904][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-18 16:03:35.905][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.906][ef$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.907][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-18 16:03:35.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-18 16:03:35.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.921][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-18 16:03:35.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-18 16:03:35.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.924][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-18 16:03:35.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-18 16:03:35.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.928][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-18 16:03:35.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-18 16:03:35.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.931][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-18 16:03:35.932][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-18 16:03:35.933][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.934][ef$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.935][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-18 16:03:35.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-18 16:03:35.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.945][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-18 16:03:35.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-18 16:03:35.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.948][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-18 16:03:35.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-18 16:03:35.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.952][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-18 16:03:35.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-18 16:03:35.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.955][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-18 16:03:35.956][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-18 16:03:35.957][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.958][ef$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.959][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-18 16:03:35.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-18 16:03:35.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.968][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-18 16:03:35.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-18 16:03:35.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.972][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-18 16:03:35.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-18 16:03:35.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.975][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-18 16:03:35.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-18 16:03:35.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.979][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-18 16:03:35.980][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-18 16:03:35.980][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.981][ef$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.982][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-18 16:03:35.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-18 16:03:35.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.992][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-18 16:03:35.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-18 16:03:35.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.995][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-18 16:03:35.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-18 16:03:35.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:35.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:35.999][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-18 16:03:36.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-18 16:03:36.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.002][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-18 16:03:36.003][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-18 16:03:36.004][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.005][ef$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.006][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-18 16:03:36.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-18 16:03:36.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.015][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-18 16:03:36.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-18 16:03:36.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.019][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-18 16:03:36.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-18 16:03:36.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.022][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-18 16:03:36.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-18 16:03:36.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.026][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-18 16:03:36.027][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-18 16:03:36.028][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.029][ef$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.029][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-18 16:03:36.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-18 16:03:36.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.039][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-18 16:03:36.040][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-18 16:03:36.045][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.045][ef$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.049][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-18 16:03:36.050][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-18 16:03:36.051][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.052][ef$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.055][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-18 16:03:36.056][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-18 16:03:36.057][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.058][ef$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.062][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-18 16:03:36.063][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-18 16:03:36.063][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.064][ef$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.068][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-18 16:03:36.069][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-18 16:03:36.070][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.071][ef$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.074][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-18 16:03:36.075][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-18 16:03:36.076][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.077][ef$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.080][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-18 16:03:36.081][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-18 16:03:36.082][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.083][ef$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.087][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-01-18 16:03:36.088][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-18 16:03:36.088][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.089][ef$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.093][ef$get] Asked field names are: description.
biodb.TRACE[2025-01-18 16:03:36.094][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-01-18 16:03:36.095][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.095][ef$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.099][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-18 16:03:36.100][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-18 16:03:36.101][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.102][ef$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.105][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-18 16:03:36.106][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-18 16:03:36.107][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.108][ef$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.112][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-18 16:03:36.112][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-18 16:03:36.113][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.114][ef$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.118][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-18 16:03:36.119][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-18 16:03:36.120][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.120][ef$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.124][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-18 16:03:36.125][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-18 16:03:36.126][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.127][ef$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.130][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-18 16:03:36.131][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-18 16:03:36.132][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.133][ef$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.136][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-18 16:03:36.137][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-18 16:03:36.138][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.139][ef$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.143][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-18 16:03:36.144][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-18 16:03:36.144][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.145][ef$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.149][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-18 16:03:36.150][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-18 16:03:36.151][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.151][ef$get] fields variable is a list.
biodb.INFO [2025-01-18 16:03:36.157][biodb::testThat]
biodb.INFO [2025-01-18 16:03:36.158][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-01-18 16:03:36.159][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-18 16:03:36.160][biodb::testThat]
biodb.DEBUG[2025-01-18 16:03:36.176][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2025-01-18 16:03:36.182][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2025-01-18 16:03:36.187][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-18 16:03:36.188][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2025-01-18 16:03:36.190][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000001".
biodb.TRACE[2025-01-18 16:03:36.191][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-01-18 16:03:36.193][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000001.xml".
biodb.DEBUG[2025-01-18 16:03:36.194][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2025-01-18 16:03:36.215][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2025-01-18 16:03:36.216][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2025-01-18 16:03:36.218][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-18 16:03:36.219][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-18 16:03:36.219][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-18 16:03:36.223][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:03:36.224][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:03:36.225][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:03:36.226][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-18 16:03:36.229][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-18 16:03:36.230][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-18 16:03:36.231][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.232][ef$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.233][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-18 16:03:36.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-18 16:03:36.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.236][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-18 16:03:36.237][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-18 16:03:36.238][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.239][ef$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.240][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-18 16:03:36.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-18 16:03:36.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.244][ef$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-18 16:03:36.244][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-18 16:03:36.245][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.246][ef$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.247][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-18 16:03:36.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-18 16:03:36.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.251][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-18 16:03:36.252][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-18 16:03:36.253][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.253][ef$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.255][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-18 16:03:36.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-18 16:03:36.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.258][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-18 16:03:36.259][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-18 16:03:36.260][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.261][ef$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.262][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-18 16:03:36.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-18 16:03:36.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.265][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-18 16:03:36.266][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-18 16:03:36.267][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.268][ef$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.269][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-18 16:03:36.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-18 16:03:36.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.273][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-18 16:03:36.274][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-18 16:03:36.274][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.275][ef$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.276][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-18 16:03:36.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-18 16:03:36.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.280][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-18 16:03:36.281][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-18 16:03:36.282][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.283][ef$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.284][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-18 16:03:36.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-18 16:03:36.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.287][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-18 16:03:36.288][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-18 16:03:36.289][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.290][ef$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.291][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-18 16:03:36.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-18 16:03:36.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.294][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-18 16:03:36.295][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-18 16:03:36.296][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.297][ef$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.298][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-18 16:03:36.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-18 16:03:36.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.306][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-18 16:03:36.307][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-18 16:03:36.308][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.309][ef$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.310][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-18 16:03:36.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-18 16:03:36.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.313][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-18 16:03:36.314][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-18 16:03:36.315][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.316][ef$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.317][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-18 16:03:36.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-18 16:03:36.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.321][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-18 16:03:36.322][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-18 16:03:36.322][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.323][ef$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.324][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-18 16:03:36.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-18 16:03:36.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.328][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-18 16:03:36.329][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-18 16:03:36.330][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.331][ef$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.332][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-18 16:03:36.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-18 16:03:36.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.335][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-18 16:03:36.336][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-18 16:03:36.337][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.338][ef$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.339][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-18 16:03:36.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-18 16:03:36.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.342][ef$get] Asked field names are: description.
biodb.TRACE[2025-01-18 16:03:36.343][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-01-18 16:03:36.344][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.345][ef$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.346][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-18 16:03:36.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-18 16:03:36.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.350][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-01-18 16:03:36.351][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-18 16:03:36.351][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.352][ef$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.353][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-18 16:03:36.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-18 16:03:36.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.357][ef$get] Asked field names are: super.class.
biodb.TRACE[2025-01-18 16:03:36.358][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-18 16:03:36.359][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.360][ef$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.361][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2025-01-18 16:03:36.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-18 16:03:36.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.364][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-18 16:03:36.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-18 16:03:36.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.368][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-18 16:03:36.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-18 16:03:36.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.371][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-18 16:03:36.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-18 16:03:36.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.375][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-18 16:03:36.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-18 16:03:36.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.378][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-18 16:03:36.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-18 16:03:36.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.382][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-01-18 16:03:36.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-01-18 16:03:36.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.385][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-18 16:03:36.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-18 16:03:36.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.389][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-18 16:03:36.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-18 16:03:36.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.392][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-18 16:03:36.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-18 16:03:36.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.396][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-18 16:03:36.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-18 16:03:36.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.399][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-18 16:03:36.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-18 16:03:36.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.403][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-01-18 16:03:36.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-01-18 16:03:36.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.406][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-18 16:03:36.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-18 16:03:36.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.410][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-18 16:03:36.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-18 16:03:36.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.413][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2025-01-18 16:03:36.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2025-01-18 16:03:36.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.417][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-18 16:03:36.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-18 16:03:36.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.420][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-18 16:03:36.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-18 16:03:36.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.424][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2025-01-18 16:03:36.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2025-01-18 16:03:36.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.431][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-18 16:03:36.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-18 16:03:36.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.435][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-18 16:03:36.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-18 16:03:36.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.438][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2025-01-18 16:03:36.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2025-01-18 16:03:36.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.442][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-01-18 16:03:36.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-18 16:03:36.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.445][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-01-18 16:03:36.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-18 16:03:36.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.449][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2025-01-18 16:03:36.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2025-01-18 16:03:36.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.452][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-18 16:03:36.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-18 16:03:36.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.456][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-18 16:03:36.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-18 16:03:36.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.459][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-18 16:03:36.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-18 16:03:36.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.463][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-18 16:03:36.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-18 16:03:36.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.466][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-18 16:03:36.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-18 16:03:36.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.470][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-18 16:03:36.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-18 16:03:36.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.473][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-18 16:03:36.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-18 16:03:36.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.477][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-18 16:03:36.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-18 16:03:36.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.480][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-18 16:03:36.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-18 16:03:36.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.484][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-18 16:03:36.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-18 16:03:36.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.487][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-18 16:03:36.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-18 16:03:36.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.491][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-18 16:03:36.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-18 16:03:36.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.494][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-18 16:03:36.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-18 16:03:36.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.498][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-18 16:03:36.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-18 16:03:36.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.501][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-01-18 16:03:36.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-01-18 16:03:36.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.505][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-18 16:03:36.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-18 16:03:36.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.508][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-18 16:03:36.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-18 16:03:36.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.512][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-01-18 16:03:36.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-01-18 16:03:36.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.515][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-18 16:03:36.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-18 16:03:36.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.519][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-18 16:03:36.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-18 16:03:36.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.522][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-18 16:03:36.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-18 16:03:36.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.526][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-18 16:03:36.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-18 16:03:36.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.529][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-18 16:03:36.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-18 16:03:36.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.533][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-18 16:03:36.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2025-01-18 16:03:36.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.536][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-18 16:03:36.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-18 16:03:36.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.540][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-18 16:03:36.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-18 16:03:36.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.543][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-18 16:03:36.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-18 16:03:36.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.547][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-18 16:03:36.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-18 16:03:36.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.550][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-18 16:03:36.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-18 16:03:36.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.557][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-01-18 16:03:36.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-01-18 16:03:36.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.561][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-01-18 16:03:36.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-18 16:03:36.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.564][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-18 16:03:36.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-18 16:03:36.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.568][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-18 16:03:36.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-18 16:03:36.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.571][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-18 16:03:36.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-18 16:03:36.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.575][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2025-01-18 16:03:36.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-18 16:03:36.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.579][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-18 16:03:36.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-18 16:03:36.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.582][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-18 16:03:36.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-18 16:03:36.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.586][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-18 16:03:36.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-18 16:03:36.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.589][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-18 16:03:36.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-18 16:03:36.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.593][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-18 16:03:36.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-18 16:03:36.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.597][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-01-18 16:03:36.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-01-18 16:03:36.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.600][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-01-18 16:03:36.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-01-18 16:03:36.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.604][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-18 16:03:36.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-18 16:03:36.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.607][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2025-01-18 16:03:36.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2025-01-18 16:03:36.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.611][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-18 16:03:36.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-18 16:03:36.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.614][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-18 16:03:36.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-18 16:03:36.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.618][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-18 16:03:36.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-18 16:03:36.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.621][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-18 16:03:36.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-18 16:03:36.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.625][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-18 16:03:36.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-18 16:03:36.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.628][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-18 16:03:36.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-18 16:03:36.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-18 16:03:36.632][self$createEntryFromContent] Accession numbers: HMDB0000001.
biodb.TRACE[2025-01-18 16:03:36.633][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-01-18 16:03:36.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-01-18 16:03:36.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.636][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-01-18 16:03:36.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-01-18 16:03:36.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.640][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-01-18 16:03:36.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-01-18 16:03:36.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-01-18 16:03:36.649][biodb::testThat]
biodb.INFO [2025-01-18 16:03:36.650][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-01-18 16:03:36.651][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-18 16:03:36.652][biodb::testThat]
biodb.TRACE[2025-01-18 16:03:36.655][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-18 16:03:36.656][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-18 16:03:36.656][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.657][ef$get] fields variable is a list.
biodb.DEBUG[2025-01-18 16:03:36.658][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "name".
biodb.TRACE[2025-01-18 16:03:36.684][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-18 16:03:36.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-18 16:03:36.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.688][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-18 16:03:36.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-18 16:03:36.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.691][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-18 16:03:36.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-18 16:03:36.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-18 16:03:36.697][function(conn, opt)] With value "1-Methylhistidine".
biodb.DEBUG[2025-01-18 16:03:36.698][private$doSearchForEntries] fields NAMES = name
biodb.DEBUG[2025-01-18 16:03:36.699][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2025-01-18 16:03:36.700][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2025-01-18 16:03:36.701][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-18 16:03:36.703][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-18 16:03:36.704][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-01-18 16:03:36.705][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-18 16:03:36.706][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-01-18 16:03:36.707][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-01-18 16:03:36.708][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-01-18 16:03:36.709][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-01-18 16:03:36.710][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2025-01-18 16:03:36.711][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2025-01-18 16:03:36.712][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2025-01-18 16:03:36.713][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-18 16:03:36.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-18 16:03:36.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.717][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-18 16:03:36.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-18 16:03:36.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.720][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-18 16:03:36.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-18 16:03:36.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.724][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-18 16:03:36.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-18 16:03:36.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-18 16:03:36.728][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2025-01-18 16:03:36.728][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2025-01-18 16:03:36.729][function(conn, opt)] With found IDs [1]: "HMDB0000001".
biodb.TRACE[2025-01-18 16:03:36.739][ef$get] Asked field names are: description.
biodb.TRACE[2025-01-18 16:03:36.740][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-01-18 16:03:36.741][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.741][ef$get] fields variable is a list.
biodb.DEBUG[2025-01-18 16:03:36.742][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "description".
biodb.TRACE[2025-01-18 16:03:36.752][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-18 16:03:36.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-18 16:03:36.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.755][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-18 16:03:36.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-18 16:03:36.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.759][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-18 16:03:36.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-18 16:03:36.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-18 16:03:36.764][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[2025-01-18 16:03:36.816][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2025-01-18 16:03:36.817][private$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[2025-01-18 16:03:36.818][private$doSearchForEntries] fields VALUES = 1-Methylhistidine, also known as 1-MHis, belongs to the class of organic compounds known as histidine and derivatives. Histidine and derivatives are compounds containing cysteine or a derivative thereof resulting from a reaction of cysteine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. 1-Methylhistidine is derived mainly from the anserine of dietary flesh sources, especially poultry. The enzyme, carnosinase, splits anserine into beta-alanine and 1-MHis. High levels of 1-MHis tend to inhibit the enzyme carnosinase and increase anserine levels. Conversely, genetic variants with deficient carnosinase activity in plasma show increased 1-MHis excretions when they consume a high meat diet. Reduced serum carnosinase activity is also found in patients with Parkinson's disease and multiple sclerosis and patients following a cerebrovascular accident. Vitamin E deficiency can lead to 1-methylhistidinuria from increased oxidative effects in skeletal muscle. 1-Methylhistidine is a biomarker for the consumption of meat, especially red meat.
biodb.DEBUG[2025-01-18 16:03:36.830][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-18 16:03:36.832][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-18 16:03:36.833][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-01-18 16:03:36.834][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-18 16:03:36.835][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-01-18 16:03:36.848][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-01-18 16:03:36.849][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-01-18 16:03:36.850][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-01-18 16:03:36.851][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2025-01-18 16:03:36.852][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2025-01-18 16:03:36.853][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2025-01-18 16:03:36.854][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-18 16:03:36.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-18 16:03:36.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.858][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-18 16:03:36.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-18 16:03:36.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.862][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-18 16:03:36.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-18 16:03:36.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.865][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2025-01-18 16:03:36.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2025-01-18 16:03:36.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-18 16:03:36.869][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2025-01-18 16:03:36.869][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2025-01-18 16:03:36.870][function(conn, opt)] With found IDs [1]: "HMDB0000001".
biodb.TRACE[2025-01-18 16:03:36.880][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-18 16:03:36.881][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-18 16:03:36.882][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.882][ef$get] fields variable is a list.
biodb.DEBUG[2025-01-18 16:03:36.883][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "secondary.accessions".
biodb.TRACE[2025-01-18 16:03:36.893][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-18 16:03:36.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-18 16:03:36.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.896][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-18 16:03:36.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-18 16:03:36.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.900][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-18 16:03:36.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-18 16:03:36.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-18 16:03:36.905][function(conn, opt)] With value "HMDB00001".
biodb.DEBUG[2025-01-18 16:03:36.906][private$doSearchForEntries] fields NAMES = secondary.accessions
biodb.DEBUG[2025-01-18 16:03:36.907][private$doSearchForEntries] fields VALUES = HMDB00001
biodb.DEBUG[2025-01-18 16:03:36.908][private$doSearchForEntries] fields VALUES = HMDB00001
biodb.DEBUG[2025-01-18 16:03:36.910][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-18 16:03:36.914][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-18 16:03:36.916][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-01-18 16:03:36.917][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-18 16:03:36.918][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-01-18 16:03:36.919][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-01-18 16:03:36.920][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-01-18 16:03:36.921][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-01-18 16:03:36.921][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2025-01-18 16:03:36.922][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2025-01-18 16:03:36.923][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2025-01-18 16:03:36.925][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-18 16:03:36.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-18 16:03:36.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.928][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-18 16:03:36.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-18 16:03:36.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.932][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-18 16:03:36.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-18 16:03:36.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.935][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-18 16:03:36.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-18 16:03:36.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-18 16:03:36.939][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2025-01-18 16:03:36.940][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2025-01-18 16:03:36.940][function(conn, opt)] With found IDs [1]: "HMDB0000001".
biodb.INFO [2025-01-18 16:03:36.952][biodb::testThat]
biodb.INFO [2025-01-18 16:03:36.953][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-01-18 16:03:36.954][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-18 16:03:36.955][biodb::testThat]
biodb.TRACE[2025-01-18 16:03:36.963][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-18 16:03:36.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-18 16:03:36.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.967][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-18 16:03:36.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-18 16:03:36.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:36.970][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-18 16:03:36.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-18 16:03:36.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:36.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-18 16:03:36.983][private$doSearchForEntries] fields NAMES = name
biodb.DEBUG[2025-01-18 16:03:36.983][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2025-01-18 16:03:36.984][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2025-01-18 16:03:36.986][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-18 16:03:36.987][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-18 16:03:36.988][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2025-01-18 16:03:36.990][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2025-01-18 16:03:36.990][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2025-01-18 16:03:36.992][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2025-01-18 16:03:36.992][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2025-01-18 16:03:36.993][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2025-01-18 16:03:36.994][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2025-01-18 16:03:36.995][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2025-01-18 16:03:36.996][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2025-01-18 16:03:36.997][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-18 16:03:36.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-18 16:03:36.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:37.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:37.001][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-18 16:03:37.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-18 16:03:37.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:37.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:37.005][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-18 16:03:37.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-18 16:03:37.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:37.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:37.008][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-18 16:03:37.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-18 16:03:37.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:37.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-18 16:03:37.012][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2025-01-18 16:03:37.012][private$doSearchForEntries] COUNT IDS = 1
biodb.INFO [2025-01-18 16:03:37.024][biodb::testThat]
biodb.INFO [2025-01-18 16:03:37.025][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-01-18 16:03:37.026][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-18 16:03:37.027][biodb::testThat]
biodb.TRACE[2025-01-18 16:03:37.048][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-18 16:03:37.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-18 16:03:37.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:37.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:37.051][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-18 16:03:37.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-18 16:03:37.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:37.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:37.055][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-01-18 16:03:37.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-01-18 16:03:37.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:37.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:37.059][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-01-18 16:03:37.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-01-18 16:03:37.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:37.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:37.098][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-18 16:03:37.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-18 16:03:37.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:37.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:37.102][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-18 16:03:37.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-18 16:03:37.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:37.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:37.106][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-01-18 16:03:37.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-01-18 16:03:37.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:37.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:37.109][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-01-18 16:03:37.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-01-18 16:03:37.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:37.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-01-18 16:03:37.117][biodb::testThat]
biodb.INFO [2025-01-18 16:03:37.118][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-01-18 16:03:37.119][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-18 16:03:37.120][biodb::testThat]
biodb.INFO [2025-01-18 16:03:37.126][biodb::testThat]
biodb.INFO [2025-01-18 16:03:37.127][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-01-18 16:03:37.128][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-18 16:03:37.129][biodb::testThat]
biodb.INFO [2025-01-18 16:03:37.135][biodb::testThat]
biodb.INFO [2025-01-18 16:03:37.136][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-01-18 16:03:37.136][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-18 16:03:37.137][biodb::testThat]
biodb.DEBUG[2025-01-18 16:03:37.140][function(conn, opt)] Trying to download "http://www.hmdb.ca/metabolites/HMDB0000001".
biodb.DEBUG[2025-01-18 16:03:55.104][getUrlContent] Use RCurl for downloading content of URL http://www.hmdb.ca/metabolites/HMDB0000001.
biodb.INFO [2025-01-18 16:03:57.203][biodb::testThat]
biodb.INFO [2025-01-18 16:03:57.206][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-01-18 16:03:57.208][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-18 16:03:57.210][biodb::testThat]
biodb.DEBUG[2025-01-18 16:03:57.580][getUrlContent] Use RCurl for downloading content of URL http://www.hmdb.ca/structures/HMDB0000001/image.png.
biodb.TRACE[2025-01-18 16:03:57.607][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-18 16:03:57.609][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-18 16:03:57.611][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:57.612][ef$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:57.614][ef$get] Asked field names are: description.
biodb.TRACE[2025-01-18 16:03:57.616][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-01-18 16:03:57.617][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:57.619][ef$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:57.636][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-18 16:03:57.637][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-18 16:03:57.639][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:57.640][ef$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:57.642][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-18 16:03:57.643][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-18 16:03:57.645][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:57.646][ef$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:57.648][ef$get] Asked field names are: description.
biodb.TRACE[2025-01-18 16:03:57.649][ef$get] Realnames of fields are: description.
biodb.TRACE[2025-01-18 16:03:57.650][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:57.652][ef$get] fields variable is a list.
biodb.TRACE[2025-01-18 16:03:57.653][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2025-01-18 16:03:57.654][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2025-01-18 16:03:57.655][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-18 16:03:57.656][ef$get] fields variable is a list.
biodb.INFO [2025-01-18 16:03:57.658][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-01-18 16:03:57.659][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler
biodb.INFO [2025-01-18 16:03:57.661][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2025-01-18 16:03:57.662][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-01-18 16:03:57.663][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-18 16:03:57.664][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-18 16:03:57.665][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-18 16:03:57.665][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-18 16:03:57.666][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-01-18 16:03:57.667][FUN] Functions in observer 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 
  4.638   0.218  25.023

'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)