Back to Long Tests report for BioC 3.20

This page was generated on 2024-05-18 23:55:02 -0400 (Sat, 18 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4666
palomino4Windows Server 2022 Datacenterx644.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 4401
merida1macOS 12.7.4 Montereyx86_644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4428
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 1.11.0  (landing page)
Pierrick Roger
Snapshot Date: 2024-05-18 09:55:01 -0400 (Sat, 18 May 2024)
git_url: https://git.bioconductor.org/packages/biodbHmdb
git_branch: devel
git_last_commit: c3d59a4
git_last_commit_date: 2024-04-30 11:39:05 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  ERROR  
palomino4Windows Server 2022 Datacenter / x64  ERROR  
merida1macOS 12.7.4 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: 1.11.0
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_1.11.0.tar.gz
StartedAt: 2024-05-18 16:07:04 -0400 (Sat, 18 May 2024)
EndedAt: 2024-05-18 16:22:34 -0400 (Sat, 18 May 2024)
EllapsedTime: 930.2 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbHmdb.Rcheck
Warnings: NA

Tests output

biodbHmdb.Rcheck/tests/testthat.Rout.fail


R version 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbHmdb)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbHmdb")
biodb.INFO [2024-05-18 16:08:13.197][biodb::testContext]
biodb.INFO [2024-05-18 16:08:13.199][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-18 16:08:13.200][biodb::testContext] Test context - Generic long tests
biodb.INFO [2024-05-18 16:08:13.201][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-18 16:08:13.202][biodb::testContext]
biodb.INFO [2024-05-18 16:08:13.208][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.13.0.
biodb.DEBUG[2024-05-18 16:08:13.210][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-05-18 16:08:13.217][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-18 16:08:13.218][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-05-18 16:08:13.219][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-05-18 16:08:13.220][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:08:13.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:08:13.221][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:08:13.222][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-05-18 16:08:13.239][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-05-18 16:08:13.240][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:08:13.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:08:13.242][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:08:13.243][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-05-18 16:08:13.243][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-05-18 16:08:13.244][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:08:13.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:08:13.246][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:08:13.247][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-05-18 16:08:13.248][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-05-18 16:08:13.249][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-05-18 16:08:13.249][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:08:13.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:08:13.251][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:08:13.252][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-05-18 16:08:13.253][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-05-18 16:08:13.254][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-05-18 16:08:13.254][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:08:13.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:08:13.256][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:08:13.257][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-05-18 16:08:13.258][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-05-18 16:08:13.258][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:08:13.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:08:13.260][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:08:13.261][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-05-18 16:08:13.262][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-05-18 16:08:13.263][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-05-18 16:08:13.263][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:08:13.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:08:13.265][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:08:13.266][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-05-18 16:08:13.267][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-05-18 16:08:13.268][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:08:13.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:08:13.269][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:08:13.270][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-05-18 16:08:13.271][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-05-18 16:08:13.272][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-05-18 16:08:13.273][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:08:13.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:08:13.274][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:08:13.275][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-05-18 16:08:13.276][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-05-18 16:08:13.277][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-05-18 16:08:13.278][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-05-18 16:08:13.279][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-05-18 16:08:13.280][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-05-18 16:08:13.280][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:08:13.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:08:13.282][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:08:13.283][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-05-18 16:08:13.284][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-05-18 16:08:13.285][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:08:13.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:08:13.286][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:08:13.287][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-05-18 16:08:13.288][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-05-18 16:08:13.289][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:08:13.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:08:13.290][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:08:13.291][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-05-18 16:08:13.292][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-05-18 16:08:13.293][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:08:13.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:08:13.294][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:08:13.295][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-05-18 16:08:13.296][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-05-18 16:08:13.297][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:08:13.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:08:13.299][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[2024-05-18 16:08:13.300][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-05-18 16:08:13.300][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-05-18 16:08:13.301][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:08:13.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:08:13.303][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:08:13.304][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-05-18 16:08:13.305][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-05-18 16:08:13.309][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-05-18 16:08:13.310][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:08:13.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:08:13.312][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:08:13.313][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-05-18 16:08:13.314][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-05-18 16:08:13.315][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-05-18 16:08:13.315][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:08:13.316][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:08:13.317][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:08:13.320][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-05-18 16:08:13.357][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-18 16:08:13.371][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-05-18 16:08:13.372][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-18 16:08:13.373][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-18 16:08:13.374][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-18 16:08:13.375][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-18 16:08:13.376][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-18 16:08:13.377][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-18 16:08:13.378][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-18 16:08:13.379][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-18 16:08:13.380][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-18 16:08:13.380][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-05-18 16:08:13.381][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-18 16:08:13.382][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:08:13.383][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-18 16:08:13.384][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-18 16:08:13.384][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-18 16:08:13.384][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-18 16:08:13.384][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-18 16:08:13.384][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-18 16:08:13.385][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-18 16:08:13.386][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-18 16:08:13.387][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-18 16:08:13.387][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-18 16:08:13.388][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-18 16:08:13.389][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-18 16:08:13.390][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-18 16:08:13.391][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:08:13.392][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-18 16:08:13.392][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-18 16:08:13.393][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-18 16:08:13.394][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:08:13.395][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-05-18 16:08:13.397][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-18 16:08:13.398][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-05-18 16:08:13.399][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-18 16:08:13.399][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-18 16:08:13.400][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-18 16:08:13.401][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-18 16:08:13.402][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-18 16:08:13.403][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-18 16:08:13.404][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-18 16:08:13.405][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-18 16:08:13.406][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-18 16:08:13.407][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-05-18 16:08:13.407][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-18 16:08:13.408][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:08:13.409][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-18 16:08:13.410][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-18 16:08:13.410][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-18 16:08:13.410][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-18 16:08:13.410][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-18 16:08:13.410][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-18 16:08:13.411][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-18 16:08:13.412][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-18 16:08:13.413][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-18 16:08:13.414][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-18 16:08:13.414][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-18 16:08:13.415][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-18 16:08:13.416][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-18 16:08:13.417][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:08:13.418][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-18 16:08:13.419][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-18 16:08:13.419][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-18 16:08:13.420][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:08:13.421][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-05-18 16:08:13.423][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-18 16:08:13.424][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-05-18 16:08:13.425][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-18 16:08:13.426][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-18 16:08:13.426][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-18 16:08:13.427][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-18 16:08:13.428][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-18 16:08:13.429][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-18 16:08:13.430][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-18 16:08:13.431][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-18 16:08:13.432][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-18 16:08:13.433][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-05-18 16:08:13.433][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-18 16:08:13.434][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:08:13.435][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-18 16:08:13.436][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:08:13.437][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-18 16:08:13.438][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-18 16:08:13.439][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-18 16:08:13.440][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-18 16:08:13.440][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-18 16:08:13.441][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-18 16:08:13.442][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-18 16:08:13.443][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:08:13.444][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-18 16:08:13.445][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-18 16:08:13.445][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-18 16:08:13.446][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:08:13.447][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-05-18 16:08:13.449][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-18 16:08:13.450][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-05-18 16:08:13.451][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-18 16:08:13.452][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-18 16:08:13.452][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-18 16:08:13.453][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-18 16:08:13.454][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-18 16:08:13.455][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-18 16:08:13.456][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-18 16:08:13.457][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-18 16:08:13.458][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-18 16:08:13.459][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-05-18 16:08:13.460][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-18 16:08:13.460][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:08:13.461][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-18 16:08:13.462][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:08:13.463][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-18 16:08:13.464][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-18 16:08:13.465][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-18 16:08:13.466][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-18 16:08:13.467][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-18 16:08:13.467][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-18 16:08:13.468][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-18 16:08:13.469][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:08:13.470][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-18 16:08:13.471][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-18 16:08:13.472][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-18 16:08:13.472][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:08:13.476][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-18 16:08:13.477][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:08:13.478][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:08:13.479][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:08:13.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:08:13.480][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:08:13.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:08:13.482][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:08:13.483][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:08:13.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:08:13.484][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:08:13.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:08:13.486][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:08:13.487][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:08:13.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:08:13.488][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:08:13.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:08:13.490][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:08:13.491][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:08:13.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:08:13.492][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:08:13.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:08:13.494][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:08:13.494][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:08:13.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:08:13.496][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:08:13.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:08:13.498][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:08:13.498][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:08:13.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:08:13.500][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:08:13.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:08:13.502][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:08:13.502][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:08:13.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:08:13.504][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:08:13.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:08:13.509][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:08:13.510][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:08:13.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:08:13.512][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:08:13.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:08:13.513][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:08:13.514][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:08:13.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:08:13.516][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:08:13.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:08:13.517][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:08:13.518][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:08:13.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:08:13.520][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:08:13.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:08:13.521][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:08:13.522][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:08:13.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:08:13.523][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:08:13.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:08:13.525][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:08:13.526][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:08:13.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:08:13.527][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:08:13.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:08:13.529][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:08:13.530][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:08:13.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:08:13.531][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:08:13.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:08:13.533][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:08:13.534][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:08:13.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:08:13.535][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:08:13.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:08:13.537][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:08:13.538][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:08:13.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:08:13.539][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:08:13.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:08:13.541][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:08:13.542][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:08:13.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:08:13.543][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:08:13.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:08:13.545][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:08:13.546][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:08:13.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:08:13.547][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:08:13.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:08:13.549][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:08:13.550][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-05-18 16:08:13.559][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-05-18 16:08:13.561][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-05-18 16:08:13.562][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-05-18 16:08:13.563][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-18 16:08:13.565][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-05-18 16:08:13.566][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-05-18 16:08:13.568][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-05-18 16:08:13.569][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-05-18 16:08:13.570][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-05-18 16:08:13.572][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-18 16:08:13.573][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-05-18 16:08:13.575][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-05-18 16:08:13.576][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-05-18 16:08:13.577][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-05-18 16:08:13.579][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-18 16:08:13.580][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-05-18 16:08:13.582][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-05-18 16:08:13.583][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-18 16:08:13.584][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-05-18 16:08:13.586][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-05-18 16:08:13.587][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-05-18 16:08:13.588][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-05-18 16:08:13.590][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-05-18 16:08:13.591][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-05-18 16:08:13.593][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-05-18 16:08:13.594][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-05-18 16:08:13.595][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-05-18 16:08:13.597][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-05-18 16:08:13.598][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-05-18 16:08:13.600][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-05-18 16:08:13.601][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-05-18 16:08:13.602][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-05-18 16:08:13.604][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-05-18 16:08:13.605][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-05-18 16:08:13.606][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-05-18 16:08:13.608][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-05-18 16:08:13.609][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-05-18 16:08:13.611][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-05-18 16:08:13.612][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-05-18 16:08:13.613][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-05-18 16:08:13.615][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-05-18 16:08:13.616][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-05-18 16:08:13.618][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-05-18 16:08:13.619][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-05-18 16:08:13.620][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-05-18 16:08:13.622][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-05-18 16:08:13.623][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-05-18 16:08:13.625][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-05-18 16:08:13.626][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-05-18 16:08:13.627][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-05-18 16:08:13.629][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-05-18 16:08:13.630][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-05-18 16:08:13.631][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-05-18 16:08:13.633][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-05-18 16:08:13.634][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-05-18 16:08:13.636][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-05-18 16:08:13.637][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-05-18 16:08:13.638][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-05-18 16:08:13.640][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-05-18 16:08:13.641][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-05-18 16:08:13.642][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-05-18 16:08:13.644][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-05-18 16:08:13.645][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-05-18 16:08:13.647][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-05-18 16:08:13.648][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-05-18 16:08:13.649][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-18 16:08:13.651][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-18 16:08:13.652][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-05-18 16:08:13.653][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-05-18 16:08:13.655][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-05-18 16:08:13.656][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-05-18 16:08:13.657][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-05-18 16:08:13.659][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-05-18 16:08:13.660][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-05-18 16:08:13.661][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-05-18 16:08:13.663][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-05-18 16:08:13.664][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-05-18 16:08:13.666][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-05-18 16:08:13.667][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-05-18 16:08:13.668][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-05-18 16:08:13.670][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-05-18 16:08:13.671][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-05-18 16:08:13.678][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-05-18 16:08:13.679][initialize] This is biodb version 1.13.0.
biodb.DEBUG[2024-05-18 16:08:13.683][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-18 16:08:13.684][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:08:13.685][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:08:13.697][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:08:13.698][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:08:13.703][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:08:13.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:08:13.705][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:08:13.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:08:13.707][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:08:13.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:08:13.708][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:08:13.709][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:08:13.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:08:13.711][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:08:13.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:08:13.713][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:08:13.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:08:13.714][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:08:13.715][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:08:13.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:08:13.717][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:08:13.718][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:08:13.719][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:08:13.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:08:13.720][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:08:13.721][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:08:13.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:08:13.723][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:08:13.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:08:13.725][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:08:13.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:08:13.727][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:08:13.728][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:08:13.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:08:13.729][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:08:13.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:08:13.731][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:08:13.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:08:13.733][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:08:13.734][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:08:13.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:08:13.735][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:08:13.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:08:13.737][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:08:13.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:08:13.739][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:08:13.739][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:08:13.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:08:13.741][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:08:13.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:08:13.743][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:08:13.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:08:13.744][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:08:13.745][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:08:13.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:08:13.747][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:08:13.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:08:13.748][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:08:13.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:08:13.750][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:08:13.751][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:08:13.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:08:13.752][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:08:13.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:08:13.754][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:08:13.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:08:13.755][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:08:13.756][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:08:13.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:08:13.758][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:08:13.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:08:13.759][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:08:13.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:08:13.761][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:08:13.762][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:08:13.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:08:13.763][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:08:13.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:08:13.765][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:08:13.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:08:13.766][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:08:13.767][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:08:13.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:08:13.769][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:08:13.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:08:13.770][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:08:13.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:08:13.772][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:08:13.773][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:08:13.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:08:13.774][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:08:13.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:08:13.776][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:08:13.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:08:13.777][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:08:13.778][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:08:13.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:08:13.780][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:08:13.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:08:13.781][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:08:13.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:08:13.783][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:08:13.784][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:08:13.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:08:13.785][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:08:13.786][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:08:13.787][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:08:13.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:08:13.788][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[2024-05-18 16:08:13.789][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:08:13.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:08:13.791][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:08:13.791][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:08:13.792][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:08:13.793][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:08:13.794][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:08:13.795][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:08:13.795][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:08:13.796][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:08:13.797][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:08:13.798][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:08:13.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:08:13.799][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:08:13.800][biodb$getConfig()$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-05-18 16:08:13.801][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:08:13.802][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:08:13.803][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:08:13.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:08:13.804][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:08:13.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:08:13.806][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:08:13.807][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/definitions.yml".
biodb.DEBUG[2024-05-18 16:08:13.816][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2024-05-18 16:08:13.818][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-18 16:08:13.819][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-05-18 16:08:13.820][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-18 16:08:13.821][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-18 16:08:13.821][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2024-05-18 16:08:13.822][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2024-05-18 16:08:13.823][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-05-18 16:08:13.824][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-18 16:08:13.825][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-05-18 16:08:13.826][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-18 16:08:13.827][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-18 16:08:13.828][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2024-05-18 16:08:13.829][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-18 16:08:13.830][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2024-05-18 16:08:13.830][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2024-05-18 16:08:13.830][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2024-05-18 16:08:13.830][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2024-05-18 16:08:13.830][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2024-05-18 16:08:13.830][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2024-05-18 16:08:13.830][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2024-05-18 16:08:13.830][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2024-05-18 16:08:13.830][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2024-05-18 16:08:13.830][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2024-05-18 16:08:13.830][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2024-05-18 16:08:13.830][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2024-05-18 16:08:13.830][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2024-05-18 16:08:13.830][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2024-05-18 16:08:13.830][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2024-05-18 16:08:13.830][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2024-05-18 16:08:13.830][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2024-05-18 16:08:13.830][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2024-05-18 16:08:13.831][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-05-18 16:08:13.831][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-18 16:08:13.831][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2024-05-18 16:08:13.831][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2024-05-18 16:08:13.832][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-05-18 16:08:13.833][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-18 16:08:13.834][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-18 16:08:13.835][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-18 16:08:13.836][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-18 16:08:13.837][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-18 16:08:13.837][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-18 16:08:13.838][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2024-05-18 16:08:13.838][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2024-05-18 16:08:13.839][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-18 16:08:13.840][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-18 16:08:13.841][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-05-18 16:08:13.842][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:08:13.847][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2024-05-18 16:08:13.848][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-05-18 16:08:13.850][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-05-18 16:08:13.851][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-18 16:08:13.856][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-18 16:08:13.878][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2024-05-18 16:08:13.879][initialize] Register connector hmdb.metabolites with the request scheduler
biodb.DEBUG[2024-05-18 16:08:13.883][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites.
biodb.DEBUG[2024-05-18 16:08:13.887][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2024-05-18 16:08:13.891][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-18 16:08:13.892][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-18 16:08:13.894][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca".
biodb.DEBUG[2024-05-18 16:08:13.894][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.INFO [2024-05-18 16:08:13.904][biodb::testThat]
biodb.INFO [2024-05-18 16:08:13.905][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-05-18 16:08:13.906][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-18 16:08:13.906][biodb::testThat]
biodb.TRACE[2024-05-18 16:08:13.910][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[2024-05-18 16:08:13.912][biodb$getFactory()$createEntryFromCo ...] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2024-05-18 16:08:13.915][biodb$getFactory()$createEntryFromCo ...] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2024-05-18 16:08:13.924][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-18 16:08:13.924][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:08:13.925][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:08:13.936][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:08:13.937][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:08:13.938][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:08:13.939][FUN] Functions in observer BiodbConfig: [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[2024-05-18 16:08:13.950][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:08:13.951][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:08:13.952][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:13.953][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:13.955][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:08:13.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:08:13.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:13.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:13.969][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-05-18 16:08:13.970][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-05-18 16:08:13.971][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:13.971][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:13.995][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-05-18 16:08:13.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-05-18 16:08:13.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:13.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:13.999][ef$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-18 16:08:14.000][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-18 16:08:14.001][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.002][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.003][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-18 16:08:14.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-18 16:08:14.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.006][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-05-18 16:08:14.007][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-05-18 16:08:14.008][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.009][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.010][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-05-18 16:08:14.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-05-18 16:08:14.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.014][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-18 16:08:14.015][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-18 16:08:14.016][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.016][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.018][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-18 16:08:14.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-18 16:08:14.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.021][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-05-18 16:08:14.022][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-05-18 16:08:14.023][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.024][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.025][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-05-18 16:08:14.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-05-18 16:08:14.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.029][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-18 16:08:14.030][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-18 16:08:14.030][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.031][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.032][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-18 16:08:14.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-18 16:08:14.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.071][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-18 16:08:14.072][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-18 16:08:14.073][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.074][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.075][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-18 16:08:14.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-18 16:08:14.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.079][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-18 16:08:14.080][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-18 16:08:14.080][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.081][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.082][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-18 16:08:14.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-18 16:08:14.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.086][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-18 16:08:14.087][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-18 16:08:14.088][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.089][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.090][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-18 16:08:14.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-18 16:08:14.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.093][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-18 16:08:14.094][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-18 16:08:14.095][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.096][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.097][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-18 16:08:14.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-18 16:08:14.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.101][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-18 16:08:14.102][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-18 16:08:14.102][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.103][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.104][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-18 16:08:14.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-18 16:08:14.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.108][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-18 16:08:14.109][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-18 16:08:14.110][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.111][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.112][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-18 16:08:14.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-18 16:08:14.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.115][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-18 16:08:14.116][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-18 16:08:14.117][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.118][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.119][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-18 16:08:14.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-18 16:08:14.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.123][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:08:14.124][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:08:14.124][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.125][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.126][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:08:14.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:08:14.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.130][ef$get] Asked field names are: description.
biodb.TRACE[2024-05-18 16:08:14.131][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-05-18 16:08:14.132][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.132][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.133][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-05-18 16:08:14.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-05-18 16:08:14.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.137][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-18 16:08:14.138][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-18 16:08:14.139][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.140][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.141][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-18 16:08:14.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-18 16:08:14.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.144][ef$get] Asked field names are: super.class.
biodb.TRACE[2024-05-18 16:08:14.145][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-05-18 16:08:14.146][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.147][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.148][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2024-05-18 16:08:14.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-05-18 16:08:14.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.152][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:08:14.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:08:14.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.155][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:08:14.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:08:14.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.159][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:08:14.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:08:14.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.191][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-18 16:08:14.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-18 16:08:14.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.198][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-18 16:08:14.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-18 16:08:14.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.202][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-18 16:08:14.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-18 16:08:14.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.205][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-05-18 16:08:14.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-05-18 16:08:14.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.209][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-05-18 16:08:14.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-05-18 16:08:14.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.212][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-05-18 16:08:14.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-05-18 16:08:14.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.216][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-18 16:08:14.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-18 16:08:14.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.219][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-18 16:08:14.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-18 16:08:14.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.223][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-18 16:08:14.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-18 16:08:14.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.226][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-05-18 16:08:14.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-05-18 16:08:14.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.230][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-05-18 16:08:14.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-05-18 16:08:14.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.233][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-05-18 16:08:14.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-05-18 16:08:14.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.237][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-18 16:08:14.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-18 16:08:14.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.241][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-18 16:08:14.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-18 16:08:14.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.244][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-18 16:08:14.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-18 16:08:14.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.248][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-18 16:08:14.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-18 16:08:14.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.251][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-18 16:08:14.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-18 16:08:14.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.255][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-18 16:08:14.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-18 16:08:14.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.258][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-05-18 16:08:14.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-05-18 16:08:14.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.262][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-05-18 16:08:14.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-05-18 16:08:14.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.265][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-05-18 16:08:14.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-05-18 16:08:14.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.269][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-05-18 16:08:14.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-05-18 16:08:14.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.272][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-05-18 16:08:14.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-05-18 16:08:14.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.276][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-05-18 16:08:14.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-05-18 16:08:14.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.279][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-18 16:08:14.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-18 16:08:14.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.283][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-18 16:08:14.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-18 16:08:14.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.286][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-18 16:08:14.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-18 16:08:14.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.290][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-18 16:08:14.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-18 16:08:14.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.294][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-18 16:08:14.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-18 16:08:14.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.297][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-18 16:08:14.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-18 16:08:14.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.301][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-18 16:08:14.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-18 16:08:14.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.304][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-18 16:08:14.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-18 16:08:14.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.308][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-18 16:08:14.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-18 16:08:14.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.311][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-18 16:08:14.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-18 16:08:14.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.315][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-18 16:08:14.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-18 16:08:14.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.318][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-18 16:08:14.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-18 16:08:14.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.322][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-18 16:08:14.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-18 16:08:14.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.325][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-18 16:08:14.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-18 16:08:14.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.332][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-18 16:08:14.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-18 16:08:14.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.335][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:08:14.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:08:14.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.339][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:08:14.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:08:14.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.342][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:08:14.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:08:14.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.346][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-18 16:08:14.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-18 16:08:14.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.350][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-18 16:08:14.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-18 16:08:14.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.353][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-18 16:08:14.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-18 16:08:14.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.357][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-05-18 16:08:14.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-05-18 16:08:14.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.360][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-05-18 16:08:14.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-05-18 16:08:14.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.364][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-05-18 16:08:14.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-05-18 16:08:14.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.367][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-18 16:08:14.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-18 16:08:14.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.371][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-18 16:08:14.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-18 16:08:14.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.374][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-18 16:08:14.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-18 16:08:14.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.378][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2024-05-18 16:08:14.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-18 16:08:14.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.381][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-18 16:08:14.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-18 16:08:14.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.385][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-18 16:08:14.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-18 16:08:14.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.388][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-18 16:08:14.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-18 16:08:14.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.392][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2024-05-18 16:08:14.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-18 16:08:14.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.411][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:08:14.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:08:14.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.414][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:08:14.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:08:14.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.418][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:08:14.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:08:14.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.421][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:08:14.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:08:14.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.425][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:08:14.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:08:14.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.428][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-05-18 16:08:14.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-05-18 16:08:14.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.432][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-05-18 16:08:14.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-05-18 16:08:14.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.435][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:08:14.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:08:14.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.439][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-05-18 16:08:14.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-05-18 16:08:14.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.442][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:08:14.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:08:14.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.446][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:08:14.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:08:14.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.449][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:08:14.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:08:14.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.453][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:08:14.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:08:14.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.460][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:08:14.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:08:14.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.463][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:08:14.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:08:14.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-18 16:08:14.467][biodb$getFactory()$createEntryFromCo ...] Accession numbers: HMDB0000001.
biodb.TRACE[2024-05-18 16:08:14.469][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-18 16:08:14.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-18 16:08:14.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.473][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-18 16:08:14.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-18 16:08:14.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.476][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-18 16:08:14.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-18 16:08:14.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.480][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-18 16:08:14.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-18 16:08:14.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.497][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:08:14.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:08:14.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.511][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-05-18 16:08:14.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-05-18 16:08:14.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.518][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:08:14.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:08:14.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.521][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:08:14.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:08:14.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.525][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:08:14.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:08:14.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.530][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:08:14.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:08:14.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.533][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:08:14.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:08:14.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.537][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:08:14.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:08:14.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.540][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-05-18 16:08:14.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-05-18 16:08:14.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.544][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-05-18 16:08:14.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-05-18 16:08:14.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.547][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-05-18 16:08:14.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-05-18 16:08:14.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.556][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:08:14.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:08:14.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.560][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:08:14.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:08:14.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.564][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:08:14.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:08:14.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.567][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:08:14.568][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:08:14.569][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.570][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.571][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:08:14.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:08:14.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.580][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-05-18 16:08:14.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-05-18 16:08:14.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.584][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-05-18 16:08:14.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-05-18 16:08:14.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.588][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-05-18 16:08:14.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-05-18 16:08:14.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.595][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-05-18 16:08:14.596][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-05-18 16:08:14.597][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.598][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.599][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-05-18 16:08:14.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-05-18 16:08:14.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.608][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-05-18 16:08:14.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-05-18 16:08:14.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.612][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-05-18 16:08:14.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-05-18 16:08:14.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.615][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-05-18 16:08:14.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-05-18 16:08:14.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.619][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-05-18 16:08:14.620][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-05-18 16:08:14.620][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.621][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.622][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-05-18 16:08:14.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-05-18 16:08:14.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.632][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-18 16:08:14.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-18 16:08:14.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.635][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-18 16:08:14.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-18 16:08:14.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.639][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-18 16:08:14.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-18 16:08:14.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.642][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-18 16:08:14.643][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-18 16:08:14.644][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.645][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.646][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-18 16:08:14.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-18 16:08:14.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.655][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-18 16:08:14.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-18 16:08:14.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.659][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-18 16:08:14.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-18 16:08:14.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.662][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-18 16:08:14.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-18 16:08:14.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.666][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-18 16:08:14.667][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-18 16:08:14.667][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.668][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.669][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-18 16:08:14.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-18 16:08:14.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.678][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-18 16:08:14.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-18 16:08:14.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.682][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-18 16:08:14.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-18 16:08:14.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.686][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-18 16:08:14.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-18 16:08:14.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.689][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-18 16:08:14.690][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-18 16:08:14.691][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.692][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.693][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-18 16:08:14.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-18 16:08:14.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.702][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:08:14.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:08:14.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.705][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:08:14.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:08:14.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.709][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:08:14.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:08:14.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.712][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:08:14.713][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:08:14.714][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.715][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.716][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:08:14.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:08:14.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.729][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-05-18 16:08:14.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-05-18 16:08:14.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.732][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-05-18 16:08:14.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-05-18 16:08:14.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.736][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-05-18 16:08:14.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-05-18 16:08:14.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.739][ef$get] Asked field names are: description.
biodb.TRACE[2024-05-18 16:08:14.740][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-05-18 16:08:14.741][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.742][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.743][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-05-18 16:08:14.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-05-18 16:08:14.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.752][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-18 16:08:14.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-18 16:08:14.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.756][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-18 16:08:14.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-18 16:08:14.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.759][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-18 16:08:14.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-18 16:08:14.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.763][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-18 16:08:14.764][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-18 16:08:14.765][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.765][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.766][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-18 16:08:14.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-18 16:08:14.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.776][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-18 16:08:14.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-18 16:08:14.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.779][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-18 16:08:14.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-18 16:08:14.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.783][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-18 16:08:14.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-18 16:08:14.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.786][ef$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-18 16:08:14.787][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-18 16:08:14.788][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.789][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.790][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-18 16:08:14.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-18 16:08:14.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.799][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-18 16:08:14.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-18 16:08:14.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.802][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-18 16:08:14.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-18 16:08:14.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.806][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-18 16:08:14.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-18 16:08:14.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.810][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-18 16:08:14.810][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-18 16:08:14.811][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.812][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.813][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-18 16:08:14.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-18 16:08:14.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.822][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-05-18 16:08:14.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-05-18 16:08:14.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.826][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-05-18 16:08:14.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-05-18 16:08:14.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.829][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-05-18 16:08:14.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-05-18 16:08:14.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.833][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-05-18 16:08:14.834][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-05-18 16:08:14.835][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.835][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.836][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-05-18 16:08:14.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-05-18 16:08:14.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.849][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-18 16:08:14.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-18 16:08:14.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.853][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-18 16:08:14.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-18 16:08:14.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.856][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-18 16:08:14.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-18 16:08:14.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.860][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-18 16:08:14.861][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-18 16:08:14.862][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.862][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.863][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-18 16:08:14.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-18 16:08:14.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.873][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-18 16:08:14.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-18 16:08:14.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.876][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-18 16:08:14.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-18 16:08:14.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.880][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-18 16:08:14.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-18 16:08:14.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.883][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-18 16:08:14.884][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-18 16:08:14.885][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.886][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.887][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-18 16:08:14.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-18 16:08:14.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.896][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-18 16:08:14.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-18 16:08:14.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.900][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-18 16:08:14.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-18 16:08:14.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.903][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-18 16:08:14.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-18 16:08:14.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.907][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-18 16:08:14.908][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-18 16:08:14.908][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.909][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.910][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-18 16:08:14.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-18 16:08:14.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.920][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-18 16:08:14.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-18 16:08:14.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.923][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-18 16:08:14.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-18 16:08:14.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.927][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-18 16:08:14.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-18 16:08:14.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.930][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-18 16:08:14.931][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-18 16:08:14.932][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.933][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.934][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-18 16:08:14.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-18 16:08:14.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.943][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-18 16:08:14.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-18 16:08:14.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.947][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-18 16:08:14.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-18 16:08:14.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.950][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-18 16:08:14.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-18 16:08:14.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.954][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-18 16:08:14.955][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-18 16:08:14.955][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.956][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.957][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-18 16:08:14.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-18 16:08:14.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.966][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-05-18 16:08:14.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-05-18 16:08:14.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.970][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-05-18 16:08:14.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-05-18 16:08:14.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.977][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-05-18 16:08:14.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-05-18 16:08:14.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.981][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-05-18 16:08:14.982][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-05-18 16:08:14.982][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.983][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.984][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-05-18 16:08:14.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-05-18 16:08:14.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:14.994][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:08:14.994][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:08:14.995][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:14.996][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:15.000][ef$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-18 16:08:15.001][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-18 16:08:15.002][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:15.002][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:15.006][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-05-18 16:08:15.007][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-05-18 16:08:15.008][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:15.008][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:15.012][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-18 16:08:15.013][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-18 16:08:15.014][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:15.015][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:15.018][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-05-18 16:08:15.019][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-05-18 16:08:15.020][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:15.021][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:15.024][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-18 16:08:15.025][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-18 16:08:15.026][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:15.027][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:15.031][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-18 16:08:15.031][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-18 16:08:15.032][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:15.033][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:15.037][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-05-18 16:08:15.038][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-05-18 16:08:15.038][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:15.039][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:15.043][ef$get] Asked field names are: description.
biodb.TRACE[2024-05-18 16:08:15.044][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-05-18 16:08:15.045][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:15.045][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:15.049][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-18 16:08:15.050][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-18 16:08:15.051][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:15.052][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:15.055][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-18 16:08:15.056][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-18 16:08:15.057][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:15.058][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:15.061][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-18 16:08:15.062][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-18 16:08:15.063][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:15.064][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:15.067][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-18 16:08:15.068][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-18 16:08:15.069][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:15.070][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:15.074][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-18 16:08:15.075][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-18 16:08:15.075][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:15.076][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:15.080][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:08:15.081][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:08:15.081][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:15.082][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:15.086][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-18 16:08:15.087][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-18 16:08:15.088][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:15.088][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:15.092][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-05-18 16:08:15.093][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-05-18 16:08:15.094][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:15.095][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:08:15.102][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-18 16:08:15.103][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-18 16:08:15.104][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:08:15.104][ef$get] fields variable is a list.
biodb.INFO [2024-05-18 16:08:15.110][biodb::testThat]
biodb.INFO [2024-05-18 16:08:15.111][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-05-18 16:08:15.112][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-18 16:08:15.113][biodb::testThat]
biodb.DEBUG[2024-05-18 16:08:15.125][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2024-05-18 16:08:15.132][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.INFO [2024-05-18 16:08:15.136][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34" for "hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34".
biodb.DEBUG[2024-05-18 16:08:15.137][self$isDownloaded] Database hmdb.metabolites has not yet been downloaded.
biodb.INFO [2024-05-18 16:08:15.138][self$download] Downloading whole database of hmdb.metabolites.
biodb.INFO [2024-05-18 16:08:15.139][private$doDownload] Downloading HMDB metabolite database at "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip" ...
biodb.DEBUG[2024-05-18 16:08:15.141][sched$downloadFile] Downloading file "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
trying URL 'http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip'
Content type 'application/zip' length 953913010 bytes (909.7 MB)
===============================================
downloaded 863.7 MB

biodb.INFO [2024-05-18 16:09:41.896][biodb::testThat]
biodb.INFO [2024-05-18 16:09:41.898][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-05-18 16:09:41.899][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-18 16:09:41.900][biodb::testThat]
biodb.TRACE[2024-05-18 16:09:41.903][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:09:41.904][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:09:41.905][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:09:41.906][ef$get] fields variable is a list.
biodb.DEBUG[2024-05-18 16:09:41.908][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "name".
biodb.DEBUG[2024-05-18 16:09:41.929][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2024-05-18 16:09:41.988][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2024-05-18 16:09:41.990][self$isDownloaded] Database hmdb.metabolites has not yet been downloaded.
biodb.INFO [2024-05-18 16:09:41.991][self$download] Downloading whole database of hmdb.metabolites.
biodb.INFO [2024-05-18 16:09:41.992][private$doDownload] Downloading HMDB metabolite database at "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip" ...
biodb.DEBUG[2024-05-18 16:09:42.005][sched$downloadFile] Downloading file "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
trying URL 'http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip'
Content type 'application/zip' length 953913010 bytes (909.7 MB)
=======
downloaded 141.5 MB

biodb.INFO [2024-05-18 16:11:06.486][biodb::testThat]
biodb.INFO [2024-05-18 16:11:06.487][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-05-18 16:11:06.488][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-18 16:11:06.489][biodb::testThat]
biodb.DEBUG[2024-05-18 16:11:06.495][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2024-05-18 16:11:06.496][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2024-05-18 16:11:06.498][self$isDownloaded] Database hmdb.metabolites has not yet been downloaded.
biodb.INFO [2024-05-18 16:11:06.499][self$download] Downloading whole database of hmdb.metabolites.
biodb.INFO [2024-05-18 16:11:06.500][private$doDownload] Downloading HMDB metabolite database at "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip" ...
biodb.DEBUG[2024-05-18 16:11:06.501][sched$downloadFile] Downloading file "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
trying URL 'http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip'
Content type 'application/zip' length 953913010 bytes (909.7 MB)
==================================================
downloaded 909.7 MB

biodb.TRACE[2024-05-18 16:12:09.694][cch$addFilesToCache] Moving files to cache [1]: "/home/biocbuild/.cache/R/biodb/tmp/hmdb.metabolites108a76f30d9dczip".
biodb.TRACE[2024-05-18 16:12:09.699][private$doAddFilesToCache] Destination files are [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip".
biodb.DEBUG[2024-05-18 16:12:09.702][cch$addFilesToCache] Done adding files.
biodb.DEBUG[2024-05-18 16:12:09.705][self$getDownloadPath] Download path of hmdb.metabolites is "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip".
biodb.DEBUG[2024-05-18 16:12:09.707][self$download] Downloading of hmdb.metabolites completed.
biodb.TRACE[2024-05-18 16:12:09.712][self$addFilesToCache] Moving files to cache [1]: "/home/biocbuild/.cache/R/biodb/tmp/marker108a746b60177marker".
biodb.TRACE[2024-05-18 16:12:09.714][private$doAddFilesToCache] Destination files are [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/downloaded.marker".
biodb.DEBUG[2024-05-18 16:12:09.744][self$addFilesToCache] Done adding files.
biodb.DEBUG[2024-05-18 16:12:09.747][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2024-05-18 16:12:09.749][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2024-05-18 16:12:09.751][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
biodb.DEBUG[2024-05-18 16:12:09.752][self$getDownloadPath] Download path of hmdb.metabolites is "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip".
biodb.DEBUG[2024-05-18 16:12:09.754][private$doExtractDownload] Unzipping /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip into /home/biocbuild/.cache/R/biodb/tmp...
biodb.DEBUG[2024-05-18 16:12:50.520][private$findXmlDatabaseFile] Found files [3]: "hmdb.metabolites108a711b58f06zip, hmdb.metabolites108a74d9c65c4zip, hmdb_metabolites.xml" into /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip.
biodb.DEBUG[2024-05-18 16:12:50.522][private$findXmlDatabaseFile] Found XML file /home/biocbuild/.cache/R/biodb/tmp/hmdb_metabolites.xml in ZIP file.
biodb.DEBUG[2024-05-18 16:12:50.523][private$doExtractDownload] Delete existing entry files in cache system.
biodb.DEBUG[2024-05-18 16:12:50.525][private$doExtractDownload] Extract entries from XML file "/home/biocbuild/.cache/R/biodb/tmp/hmdb_metabolites.xml", into "/home/biocbuild/.cache/R/biodb/tmp".
biodb.TRACE[2024-05-18 16:22:24.421][self$addFilesToCache] Moving files to cache [217920]: "/home/biocbuild/.cache/R/biodb/tmp/HMDB0000001.xml, /home/biocbuild/.cache/R/biodb/tmp/HMDB0000002.xml, /home/biocbuild/.cache/R/biodb/tmp/HMDB0000005.xml, /home/biocbuild/.cache/R/biodb/tmp/HMDB0000008.xml, /home/biocbuild/.cache/R/biodb/tmp/HMDB0000010.xml, /home/biocbuild/.cache/R/biodb/tmp/HMDB0000011.xml, /home/biocbuild/.cache/R/biodb/tmp/HMDB0000012.xml, /home/biocbuild/.cache/R/biodb/tmp/HMDB0000014.xml, /home/biocbuild/.cache/R/biodb/tmp/HMDB0000015.xml, /home/biocbuild/.cache/R/biodb/tmp/HMDB0000016.xml, ...".
biodb.TRACE[2024-05-18 16:22:25.122][private$doAddFilesToCache] Destination files are [217920]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000001.xml, /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000002.xml, /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000005.xml, /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000008.xml, /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000010.xml, /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000011.xml, /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000012.xml, /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000014.xml, /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000015.xml, /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000016.xml, ...".
biodb.DEBUG[2024-05-18 16:22:28.997][self$addFilesToCache] Done adding files.
biodb.DEBUG[2024-05-18 16:22:28.998][private$doExtractDownload] Delete extracted database.
biodb.TRACE[2024-05-18 16:22:29.819][self$addFilesToCache] Moving files to cache [1]: "/home/biocbuild/.cache/R/biodb/tmp/marker108a71b6a6acmarker".
biodb.TRACE[2024-05-18 16:22:29.820][private$doAddFilesToCache] Destination files are [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/extracted.marker".
biodb.DEBUG[2024-05-18 16:22:29.821][self$addFilesToCache] Done adding files.
biodb.TRACE[2024-05-18 16:22:29.823][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000001".
biodb.TRACE[2024-05-18 16:22:29.824][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-18 16:22:29.826][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000001.xml".
biodb.DEBUG[2024-05-18 16:22:29.827][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2024-05-18 16:22:29.848][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2024-05-18 16:22:29.849][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2024-05-18 16:22:29.851][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-18 16:22:29.852][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:22:29.852][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:22:29.856][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:22:29.857][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:22:29.858][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:22:29.859][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-18 16:22:29.863][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:22:29.864][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:22:29.865][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:29.865][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:29.866][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:22:29.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:22:29.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:29.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:29.870][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-05-18 16:22:29.871][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-05-18 16:22:29.872][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:29.873][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:29.874][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-05-18 16:22:29.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-05-18 16:22:29.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:29.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:29.877][ef$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-18 16:22:29.878][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-18 16:22:29.879][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:29.880][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:29.881][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-18 16:22:29.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-18 16:22:29.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:29.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:29.885][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-05-18 16:22:29.886][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-05-18 16:22:29.886][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:29.887][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:29.888][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-05-18 16:22:29.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-05-18 16:22:29.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:29.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:29.892][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-18 16:22:29.893][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-18 16:22:29.894][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:29.895][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:29.896][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-18 16:22:29.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-18 16:22:29.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:29.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:29.899][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-05-18 16:22:29.900][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-05-18 16:22:29.901][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:29.902][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:29.903][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-05-18 16:22:29.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-05-18 16:22:29.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:29.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:29.907][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-18 16:22:29.908][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-18 16:22:29.909][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:29.909][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:29.911][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-18 16:22:29.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-18 16:22:29.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:29.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:29.914][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-18 16:22:29.915][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-18 16:22:29.916][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:29.917][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:29.918][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-18 16:22:29.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-18 16:22:29.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:29.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:29.922][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-18 16:22:29.923][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-18 16:22:29.923][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:29.924][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:29.926][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-18 16:22:29.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-18 16:22:29.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:29.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:29.930][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-18 16:22:29.931][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-18 16:22:29.932][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:29.933][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:29.934][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-18 16:22:29.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-18 16:22:29.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:29.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:29.938][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-18 16:22:29.939][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-18 16:22:29.940][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:29.941][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:29.942][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-18 16:22:29.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-18 16:22:29.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:29.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:29.946][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-18 16:22:29.947][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-18 16:22:29.948][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:29.949][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:29.950][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-18 16:22:29.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-18 16:22:29.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:29.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:29.954][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-18 16:22:29.955][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-18 16:22:29.956][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:29.957][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:29.959][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-18 16:22:29.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-18 16:22:29.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:29.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:29.963][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-18 16:22:29.964][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-18 16:22:29.965][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:29.966][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:29.967][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-18 16:22:29.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-18 16:22:29.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:29.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:29.971][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:22:29.972][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:22:29.973][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:29.974][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:29.975][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:22:29.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:22:29.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:29.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:29.979][ef$get] Asked field names are: description.
biodb.TRACE[2024-05-18 16:22:29.980][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-05-18 16:22:29.981][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:29.982][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:29.984][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-05-18 16:22:29.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-05-18 16:22:29.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:29.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:29.988][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-18 16:22:29.989][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-18 16:22:29.990][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:29.991][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:29.992][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-18 16:22:29.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-18 16:22:29.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:29.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:29.996][ef$get] Asked field names are: super.class.
biodb.TRACE[2024-05-18 16:22:29.997][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-05-18 16:22:29.998][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:29.999][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:30.000][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2024-05-18 16:22:30.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-05-18 16:22:30.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:30.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:30.005][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:22:30.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:22:30.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:30.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:30.009][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:22:30.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:22:30.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:30.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:30.013][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:22:30.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:22:30.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:30.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:30.017][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-18 16:22:30.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-18 16:22:30.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:30.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:30.021][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-18 16:22:30.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-18 16:22:30.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:30.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:30.025][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-18 16:22:30.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-18 16:22:30.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:30.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:30.029][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-05-18 16:22:30.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-05-18 16:22:30.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:30.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:30.033][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-05-18 16:22:30.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-05-18 16:22:30.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:30.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:30.037][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-05-18 16:22:30.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-05-18 16:22:30.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:30.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:30.041][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-18 16:22:30.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-18 16:22:30.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:30.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:30.045][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-18 16:22:30.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-18 16:22:30.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:30.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:30.049][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-18 16:22:30.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-18 16:22:30.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:30.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:30.053][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-05-18 16:22:30.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-05-18 16:22:30.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:30.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:30.057][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-05-18 16:22:30.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-05-18 16:22:30.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:30.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:30.061][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-05-18 16:22:30.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-05-18 16:22:30.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:30.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:30.065][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-18 16:22:30.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-18 16:22:30.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:30.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:30.069][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-18 16:22:30.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-18 16:22:30.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:30.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:30.073][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-05-18 16:22:30.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-05-18 16:22:30.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:30.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:30.077][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-18 16:22:30.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-18 16:22:30.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:30.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:30.081][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-18 16:22:30.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-18 16:22:30.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:30.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:30.085][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-05-18 16:22:30.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-05-18 16:22:30.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:30.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:30.089][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-05-18 16:22:30.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-05-18 16:22:30.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:30.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:30.093][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-05-18 16:22:30.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-05-18 16:22:30.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:30.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:30.097][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-05-18 16:22:30.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-05-18 16:22:30.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:30.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:30.101][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-05-18 16:22:30.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-05-18 16:22:30.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:30.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:30.105][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-05-18 16:22:30.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-05-18 16:22:30.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:30.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:30.109][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-05-18 16:22:30.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-05-18 16:22:30.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:30.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:30.113][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-18 16:22:30.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-18 16:22:30.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:30.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:30.117][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-18 16:22:30.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-18 16:22:30.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:30.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:30.121][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-18 16:22:30.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-18 16:22:30.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:30.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:30.125][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-18 16:22:30.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-18 16:22:30.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:30.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:30.129][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-18 16:22:30.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-18 16:22:30.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:30.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:30.133][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-18 16:22:30.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-18 16:22:30.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:30.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:30.137][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-18 16:22:30.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-18 16:22:30.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:30.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:30.141][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-18 16:22:30.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-18 16:22:30.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:30.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:30.145][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-18 16:22:30.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-18 16:22:30.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:30.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:30.149][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-18 16:22:30.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-18 16:22:30.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:30.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:30.153][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-18 16:22:30.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-18 16:22:30.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:30.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:30.157][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-18 16:22:30.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-18 16:22:30.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:30.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:30.161][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-18 16:22:30.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-18 16:22:30.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:30.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:30.165][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-18 16:22:30.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-18 16:22:30.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:30.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:30.211][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-18 16:22:30.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-18 16:22:30.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:30.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:30.215][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:22:30.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:22:30.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:30.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:30.218][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:22:30.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:22:30.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:30.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:30.222][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:22:30.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:22:30.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:30.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:30.225][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-18 16:22:30.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-18 16:22:30.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:30.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:30.229][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-18 16:22:30.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-18 16:22:30.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:30.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:30.232][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-18 16:22:30.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-05-18 16:22:30.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:30.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:30.236][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-05-18 16:22:30.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-05-18 16:22:30.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:30.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:30.239][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-05-18 16:22:30.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-05-18 16:22:30.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:30.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:30.242][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-05-18 16:22:30.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-05-18 16:22:30.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:30.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:30.246][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-18 16:22:30.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-18 16:22:30.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:30.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:30.249][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-18 16:22:30.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-18 16:22:30.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:30.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:30.253][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-18 16:22:30.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-18 16:22:30.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:30.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:30.256][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2024-05-18 16:22:30.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-18 16:22:30.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:30.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:30.260][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-18 16:22:30.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-18 16:22:30.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:30.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:30.263][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-18 16:22:30.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-18 16:22:30.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:30.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:30.267][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-18 16:22:30.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-18 16:22:30.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:30.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:30.270][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2024-05-18 16:22:30.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-18 16:22:30.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:30.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:30.274][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:22:30.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:22:30.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:30.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:30.278][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:22:30.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:22:30.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:30.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:30.281][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:22:30.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:22:30.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:30.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:30.285][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:22:30.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:22:30.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:30.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:30.288][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:22:30.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:22:30.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:30.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:30.292][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-05-18 16:22:30.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-05-18 16:22:30.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:30.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:30.295][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-05-18 16:22:30.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-05-18 16:22:30.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:30.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:30.299][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:22:30.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:22:30.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:30.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:30.302][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-05-18 16:22:30.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-05-18 16:22:30.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:30.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:30.306][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:22:30.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:22:30.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:30.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:30.309][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:22:30.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:22:30.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:30.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:30.313][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:22:30.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:22:30.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:30.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:30.316][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:22:30.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:22:30.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:30.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:30.320][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:22:30.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:22:30.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:30.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:30.323][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:22:30.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:22:30.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:30.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-18 16:22:30.327][self$createEntryFromContent] Accession numbers: HMDB0000001.
biodb.TRACE[2024-05-18 16:22:30.331][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:22:30.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:22:30.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:30.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:30.334][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:22:30.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:22:30.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:30.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:30.338][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:22:30.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:22:30.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:30.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-18 16:22:30.363][private$doSearchForEntries] fields NAMES = name
biodb.DEBUG[2024-05-18 16:22:30.364][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2024-05-18 16:22:30.365][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2024-05-18 16:22:30.366][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-05-18 16:22:30.368][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-05-18 16:22:30.369][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2024-05-18 16:22:30.370][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-05-18 16:22:30.371][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2024-05-18 16:22:30.372][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2024-05-18 16:22:31.225][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2024-05-18 16:22:31.226][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml, HMDB0000005.xml, HMDB0000008.xml, HMDB0000010.xml, HMDB0000011.xml
biodb.DEBUG[2024-05-18 16:22:31.398][private$doGetEntryIds] COUNT IDS = 217920
biodb.DEBUG[2024-05-18 16:22:31.454][private$doSearchForEntries] All IDs = [217920]: "HMDB0000001, HMDB0000002, HMDB0000005, HMDB0000008, HMDB0000010, HMDB0000011, HMDB0000012, HMDB0000014, HMDB0000015, HMDB0000016, ..."
biodb.DEBUG[2024-05-18 16:22:31.455][private$doSearchForEntries] Total number of IDs = 217920
biodb.TRACE[2024-05-18 16:22:31.457][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:22:31.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:22:31.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:31.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:31.460][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:22:31.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:22:31.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:31.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:31.464][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:22:31.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:22:31.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:31.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:31.467][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:22:31.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:22:31.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:31.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-18 16:22:31.471][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2024-05-18 16:22:31.472][private$doSearchForEntries] COUNT IDS = 1
biodb.INFO [2024-05-18 16:22:31.483][biodb::testThat]
biodb.INFO [2024-05-18 16:22:31.484][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-05-18 16:22:31.485][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-18 16:22:31.486][biodb::testThat]
biodb.TRACE[2024-05-18 16:22:31.503][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-18 16:22:31.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-18 16:22:31.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:31.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:31.506][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-18 16:22:31.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-18 16:22:31.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:31.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:31.510][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-18 16:22:31.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-18 16:22:31.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:31.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:31.513][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-18 16:22:31.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-18 16:22:31.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:31.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:31.552][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-18 16:22:31.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-18 16:22:31.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:31.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:31.555][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-18 16:22:31.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-18 16:22:31.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:31.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:31.559][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-18 16:22:31.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-18 16:22:31.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:31.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:31.562][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-18 16:22:31.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-18 16:22:31.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:31.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-18 16:22:31.570][biodb::testThat]
biodb.INFO [2024-05-18 16:22:31.571][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-05-18 16:22:31.572][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-18 16:22:31.573][biodb::testThat]
biodb.INFO [2024-05-18 16:22:31.579][biodb::testThat]
biodb.INFO [2024-05-18 16:22:31.580][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-05-18 16:22:31.581][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-18 16:22:31.582][biodb::testThat]
biodb.INFO [2024-05-18 16:22:31.588][biodb::testThat]
biodb.INFO [2024-05-18 16:22:31.589][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-05-18 16:22:31.589][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-18 16:22:31.590][biodb::testThat]
biodb.DEBUG[2024-05-18 16:22:31.593][function(conn, opt)] Trying to download "http://www.hmdb.ca/metabolites/HMDB0000001".
biodb.DEBUG[2024-05-18 16:22:32.741][getUrlContent] Use RCurl for downloading content of URL http://www.hmdb.ca/metabolites/HMDB0000001.
biodb.INFO [2024-05-18 16:22:32.790][biodb::testThat]
biodb.INFO [2024-05-18 16:22:32.792][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-05-18 16:22:32.794][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-18 16:22:32.796][biodb::testThat]
biodb.DEBUG[2024-05-18 16:22:33.167][getUrlContent] Use RCurl for downloading content of URL http://www.hmdb.ca/structures/HMDB0000001/image.png.
biodb.TRACE[2024-05-18 16:22:33.195][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:22:33.198][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:22:33.200][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:33.202][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:33.205][ef$get] Asked field names are: description.
biodb.TRACE[2024-05-18 16:22:33.207][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-05-18 16:22:33.209][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:33.211][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:33.214][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-05-18 16:22:33.216][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-05-18 16:22:33.218][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:33.220][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:33.222][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:22:33.224][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:22:33.226][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:33.228][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:33.229][ef$get] Asked field names are: description.
biodb.TRACE[2024-05-18 16:22:33.231][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-05-18 16:22:33.233][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:33.234][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:22:33.236][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-05-18 16:22:33.237][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-05-18 16:22:33.239][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:22:33.240][ef$get] fields variable is a list.
biodb.INFO [2024-05-18 16:22:33.242][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-05-18 16:22:33.245][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler
biodb.INFO [2024-05-18 16:22:33.247][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2024-05-18 16:22:33.248][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-05-18 16:22:33.249][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:22:33.250][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:22:33.251][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:22:33.252][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:22:33.253][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:22:33.255][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 2 | WARN 4 | SKIP 0 | PASS 124 ]

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

[ FAIL 2 | WARN 4 | SKIP 0 | PASS 124 ]
Error: Test failures
Execution halted

'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_1.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc-longtests/meat/biodbHmdb.Rcheck’
* using R version 4.4.0 RC (2024-04-16 r86468)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 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 ‘1.11.0’
* 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 11.4.0-1ubuntu1~22.04) 11.4.0’
* checking installed package size ... NOTE
  installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘zip’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘HmdbMetabolitesConn’ ‘HmdbMetabolitesEntry’ ‘hmdbToSqlite’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘longtests/testthat.R’ failed.
Last 13 lines of output:
       ▆
    1. ├─base::do.call(fct, params)
    2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
    3.   └─conn$getEntry(id, drop = TRUE)
    4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
    5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
    6.         └─conn$getEntryContent(ids)
    7.           └─self$download()
    8.             └─private$doDownload()
    9.               └─sched$downloadFile(url = zip.url, dest.file = tmpFile)
   10.                 └─utils::download.file(...)
  
  [ FAIL 2 | WARN 4 | SKIP 0 | PASS 124 ]
  Error: Test failures
  Execution halted
* DONE

Status: 1 ERROR, 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 11.4.0-1ubuntu1~22.04) 11.4.0’
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)