Back to Long Tests report for BioC 3.19

This page was generated on 2024-07-13 23:55 -0400 (Sat, 13 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4741
palomino7Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4483
merida1macOS 12.7.4 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4512
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 8/33HostnameOS / ArchCHECK
biodbHmdb 1.10.0  (landing page)
Pierrick Roger
Snapshot Date: 2024-07-13 09:55 -0400 (Sat, 13 Jul 2024)
git_url: https://git.bioconductor.org/packages/biodbHmdb
git_branch: RELEASE_3_19
git_last_commit: a7f41b2
git_last_commit_date: 2024-04-30 11:39:05 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  ERROR  
palomino7Windows Server 2022 Datacenter / x64  ERROR  
merida1macOS 12.7.4 Monterey / x86_64  ERROR  

CHECK results for biodbHmdb on palomino7

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: 1.10.0
Command: E:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbHmdb_1.10.0.tar.gz
StartedAt: 2024-07-13 16:03:28 -0400 (Sat, 13 Jul 2024)
EndedAt: 2024-07-13 16:08:42 -0400 (Sat, 13 Jul 2024)
EllapsedTime: 313.4 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbHmdb.Rcheck
Warnings: NA

Tests output

biodbHmdb.Rcheck/tests/testthat.Rout.fail


R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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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 [2024-07-13 16:05:02.749][biodb::testContext]
biodb.INFO [2024-07-13 16:05:02.752][biodb::testContext] ********************************************************************************
biodb.INFO [2024-07-13 16:05:02.753][biodb::testContext] Test context - Generic long tests
biodb.INFO [2024-07-13 16:05:02.754][biodb::testContext] ********************************************************************************
biodb.INFO [2024-07-13 16:05:02.755][biodb::testContext]
biodb.INFO [2024-07-13 16:05:02.762][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-07-13 16:05:02.764][self$loadDefinitions] Load definitions from file "E:/biocbuild/bbs-3.19-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2024-07-13 16:05:02.771][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-13 16:05:02.773][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-07-13 16:05:02.774][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-07-13 16:05:02.775][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:05:02.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:05:02.777][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:05:02.778][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-07-13 16:05:02.794][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-07-13 16:05:02.795][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:05:02.796][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:05:02.798][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:05:02.799][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-07-13 16:05:02.800][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-07-13 16:05:02.801][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:05:02.802][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:05:02.803][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:05:02.804][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-07-13 16:05:02.805][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-07-13 16:05:02.807][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-07-13 16:05:02.808][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:05:02.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:05:02.810][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:05:02.811][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-07-13 16:05:02.812][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-07-13 16:05:02.814][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-07-13 16:05:02.815][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:05:02.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:05:02.817][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:05:02.818][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-07-13 16:05:02.819][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-07-13 16:05:02.820][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:05:02.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:05:02.823][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:05:02.824][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-07-13 16:05:02.825][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-07-13 16:05:02.826][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-07-13 16:05:02.827][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:05:02.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:05:02.829][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:05:02.830][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-07-13 16:05:02.832][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-07-13 16:05:02.833][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:05:02.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:05:02.835][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:05:02.836][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-07-13 16:05:02.837][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-07-13 16:05:02.838][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-07-13 16:05:02.839][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:05:02.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:05:02.842][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:05:02.843][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-07-13 16:05:02.844][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-07-13 16:05:02.845][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-07-13 16:05:02.846][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-07-13 16:05:02.848][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-07-13 16:05:02.849][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-07-13 16:05:02.850][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:05:02.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:05:02.852][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:05:02.853][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-07-13 16:05:02.854][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-07-13 16:05:02.856][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:05:02.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:05:02.858][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:05:02.859][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-07-13 16:05:02.860][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-07-13 16:05:02.861][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:05:02.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:05:02.863][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:05:02.864][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-07-13 16:05:02.866][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-07-13 16:05:02.867][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:05:02.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:05:02.869][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:05:02.870][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-07-13 16:05:02.871][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-07-13 16:05:02.872][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:05:02.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:05:02.874][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:05:02.876][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-07-13 16:05:02.877][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-07-13 16:05:02.878][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:05:02.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:05:02.880][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:05:02.881][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-07-13 16:05:02.882][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-07-13 16:05:02.886][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-07-13 16:05:02.887][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:05:02.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:05:02.889][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:05:02.890][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-07-13 16:05:02.891][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-07-13 16:05:02.893][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-07-13 16:05:02.894][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:05:02.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:05:02.896][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:05:02.899][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-07-13 16:05:02.933][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-13 16:05:02.947][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-07-13 16:05:02.948][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-13 16:05:02.950][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-13 16:05:02.951][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-13 16:05:02.952][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-13 16:05:02.953][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-13 16:05:02.954][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-13 16:05:02.956][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-13 16:05:02.957][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-13 16:05:02.958][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-13 16:05:02.959][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-07-13 16:05:02.960][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-13 16:05:02.962][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:05:02.963][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-13 16:05:02.964][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-13 16:05:02.964][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-13 16:05:02.964][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-13 16:05:02.964][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-07-13 16:05:02.964][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-07-13 16:05:02.965][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-13 16:05:02.966][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-13 16:05:02.967][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-13 16:05:02.969][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-13 16:05:02.970][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-13 16:05:02.971][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-13 16:05:02.972][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-13 16:05:02.973][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:05:02.974][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-13 16:05:02.975][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-13 16:05:02.976][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-13 16:05:02.978][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:05:02.979][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-07-13 16:05:02.981][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-13 16:05:02.982][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-07-13 16:05:02.983][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-13 16:05:02.984][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-13 16:05:02.986][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-13 16:05:02.987][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-13 16:05:02.988][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-13 16:05:02.989][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-13 16:05:02.990][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-07-13 16:05:02.991][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-13 16:05:02.993][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-13 16:05:02.994][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-07-13 16:05:02.995][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-13 16:05:02.996][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:05:02.997][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-13 16:05:02.998][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-13 16:05:02.998][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-13 16:05:02.998][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-13 16:05:02.998][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-07-13 16:05:02.998][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-07-13 16:05:03.000][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-13 16:05:03.001][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-13 16:05:03.002][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-13 16:05:03.003][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-13 16:05:03.004][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-13 16:05:03.005][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-13 16:05:03.006][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-13 16:05:03.008][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:05:03.009][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-13 16:05:03.010][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-13 16:05:03.011][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-13 16:05:03.012][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:05:03.013][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-07-13 16:05:03.015][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-07-13 16:05:03.016][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-07-13 16:05:03.018][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-13 16:05:03.019][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-13 16:05:03.020][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-13 16:05:03.021][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-13 16:05:03.022][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-13 16:05:03.023][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-13 16:05:03.025][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-13 16:05:03.026][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-13 16:05:03.027][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-07-13 16:05:03.028][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-07-13 16:05:03.029][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-13 16:05:03.031][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:05:03.032][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-13 16:05:03.033][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:05:03.034][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-13 16:05:03.035][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-13 16:05:03.036][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-13 16:05:03.037][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-13 16:05:03.039][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-13 16:05:03.040][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-13 16:05:03.041][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-13 16:05:03.042][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:05:03.043][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-13 16:05:03.044][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-13 16:05:03.045][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-13 16:05:03.046][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:05:03.048][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-07-13 16:05:03.050][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-07-13 16:05:03.051][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-07-13 16:05:03.052][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-13 16:05:03.053][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-13 16:05:03.054][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-13 16:05:03.055][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-13 16:05:03.057][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-13 16:05:03.058][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-13 16:05:03.059][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-07-13 16:05:03.060][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-13 16:05:03.061][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-07-13 16:05:03.062][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-07-13 16:05:03.064][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-13 16:05:03.065][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:05:03.066][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-13 16:05:03.067][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:05:03.068][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-13 16:05:03.069][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-13 16:05:03.071][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-13 16:05:03.072][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-13 16:05:03.073][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-13 16:05:03.074][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-13 16:05:03.075][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-13 16:05:03.076][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:05:03.077][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-13 16:05:03.078][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-13 16:05:03.080][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-13 16:05:03.081][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:05:03.084][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-13 16:05:03.085][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:05:03.086][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:05:03.087][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:05:03.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:05:03.089][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:05:03.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:05:03.091][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:05:03.093][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:05:03.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:05:03.095][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:05:03.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:05:03.097][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:05:03.098][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:05:03.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:05:03.100][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:05:03.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:05:03.102][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:05:03.103][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:05:03.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:05:03.105][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:05:03.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:05:03.107][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:05:03.109][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:05:03.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:05:03.111][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:05:03.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:05:03.113][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:05:03.114][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:05:03.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:05:03.121][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:05:03.122][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:05:03.123][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:05:03.124][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:05:03.125][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:05:03.126][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:05:03.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:05:03.128][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:05:03.129][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:05:03.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:05:03.131][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:05:03.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:05:03.134][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:05:03.135][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:05:03.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:05:03.137][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:05:03.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:05:03.139][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:05:03.140][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:05:03.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:05:03.142][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:05:03.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:05:03.144][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:05:03.145][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:05:03.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:05:03.147][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:05:03.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:05:03.150][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:05:03.151][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:05:03.152][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:05:03.153][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:05:03.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:05:03.155][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:05:03.156][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:05:03.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:05:03.158][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:05:03.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:05:03.161][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:05:03.162][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:05:03.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:05:03.164][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:05:03.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:05:03.166][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:05:03.167][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:05:03.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:05:03.169][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:05:03.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:05:03.171][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:05:03.172][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:05:03.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:05:03.174][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:05:03.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:05:03.176][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:05:03.177][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:05:03.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:05:03.180][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:05:03.181][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:05:03.182][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:05:03.183][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-07-13 16:05:03.187][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-07-13 16:05:03.189][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-07-13 16:05:03.190][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-07-13 16:05:03.192][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-07-13 16:05:03.193][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-07-13 16:05:03.195][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-07-13 16:05:03.196][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-07-13 16:05:03.198][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-07-13 16:05:03.199][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-07-13 16:05:03.201][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-07-13 16:05:03.202][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-07-13 16:05:03.204][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-07-13 16:05:03.205][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-07-13 16:05:03.207][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-07-13 16:05:03.208][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-07-13 16:05:03.210][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-07-13 16:05:03.211][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-07-13 16:05:03.213][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-07-13 16:05:03.215][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-07-13 16:05:03.216][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-07-13 16:05:03.218][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-07-13 16:05:03.219][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-07-13 16:05:03.221][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-07-13 16:05:03.222][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-07-13 16:05:03.224][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-07-13 16:05:03.225][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-07-13 16:05:03.227][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-07-13 16:05:03.228][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-07-13 16:05:03.230][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-07-13 16:05:03.231][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-07-13 16:05:03.233][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-07-13 16:05:03.234][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-07-13 16:05:03.236][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-07-13 16:05:03.238][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-07-13 16:05:03.239][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-07-13 16:05:03.241][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-07-13 16:05:03.242][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-07-13 16:05:03.244][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-07-13 16:05:03.245][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-07-13 16:05:03.247][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-07-13 16:05:03.248][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-07-13 16:05:03.250][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-07-13 16:05:03.251][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-07-13 16:05:03.253][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-07-13 16:05:03.254][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-07-13 16:05:03.256][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-07-13 16:05:03.258][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-07-13 16:05:03.259][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-07-13 16:05:03.261][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-07-13 16:05:03.262][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-07-13 16:05:03.264][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-07-13 16:05:03.265][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-07-13 16:05:03.267][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-07-13 16:05:03.268][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-07-13 16:05:03.270][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-07-13 16:05:03.271][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-07-13 16:05:03.273][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-07-13 16:05:03.274][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-07-13 16:05:03.276][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-07-13 16:05:03.278][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-07-13 16:05:03.279][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-07-13 16:05:03.281][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-07-13 16:05:03.282][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-07-13 16:05:03.284][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-07-13 16:05:03.285][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-07-13 16:05:03.287][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-07-13 16:05:03.288][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-07-13 16:05:03.290][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-07-13 16:05:03.291][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-07-13 16:05:03.293][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-07-13 16:05:03.294][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-07-13 16:05:03.296][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-07-13 16:05:03.297][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-07-13 16:05:03.299][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-07-13 16:05:03.301][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-07-13 16:05:03.302][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-07-13 16:05:03.304][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-07-13 16:05:03.305][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-07-13 16:05:03.307][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-07-13 16:05:03.308][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-07-13 16:05:03.310][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-07-13 16:05:03.311][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-07-13 16:05:03.340][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-07-13 16:05:03.342][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-07-13 16:05:03.345][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-13 16:05:03.347][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:05:03.348][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:05:03.349][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:05:03.350][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:05:03.354][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:05:03.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:05:03.357][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:05:03.358][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:05:03.359][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:05:03.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:05:03.361][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:05:03.362][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:05:03.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:05:03.364][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:05:03.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:05:03.366][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:05:03.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:05:03.369][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:05:03.370][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:05:03.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:05:03.372][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:05:03.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:05:03.374][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:05:03.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:05:03.376][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:05:03.377][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:05:03.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:05:03.380][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:05:03.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:05:03.382][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:05:03.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:05:03.384][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:05:03.385][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:05:03.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:05:03.387][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:05:03.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:05:03.389][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:05:03.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:05:03.391][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:05:03.393][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:05:03.394][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:05:03.395][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:05:03.396][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:05:03.397][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:05:03.398][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:05:03.399][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:05:03.400][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:05:03.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:05:03.402][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:05:03.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:05:03.404][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:05:03.405][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:05:03.406][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:05:03.408][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:05:03.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:05:03.410][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:05:03.411][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:05:03.412][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:05:03.413][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:05:03.414][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:05:03.415][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:05:03.416][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:05:03.417][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:05:03.418][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:05:03.419][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:05:03.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:05:03.422][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:05:03.423][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:05:03.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:05:03.425][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:05:03.426][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:05:03.427][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:05:03.428][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:05:03.429][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:05:03.430][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:05:03.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:05:03.432][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:05:03.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:05:03.435][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:05:03.436][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:05:03.437][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:05:03.438][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:05:03.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:05:03.440][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:05:03.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:05:03.442][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:05:03.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:05:03.444][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:05:03.445][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:05:03.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:05:03.448][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:05:03.449][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:05:03.450][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:05:03.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:05:03.452][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:05:03.453][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:05:03.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:05:03.455][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:05:03.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:05:03.457][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:05:03.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:05:03.459][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:05:03.460][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:05:03.462][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:05:03.463][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:05:03.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:05:03.465][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:05:03.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:05:03.467][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:05:03.469][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:05:03.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:05:03.472][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:05:03.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:05:03.474][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:05:03.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:05:03.476][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:05:03.477][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:05:03.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:05:03.479][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:05:03.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:05:03.482][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:05:03.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:05:03.484][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:05:03.485][biodb$getConfig()$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-07-13 16:05:03.486][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:05:03.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:05:03.488][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:05:03.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:05:03.490][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:05:03.492][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:05:03.493][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:05:03.496][biodb$loadDefinitions] Load definitions from file "E:/biocbuild/bbs-3.19-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/definitions.yml".
biodb.DEBUG[2024-07-13 16:05:03.505][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2024-07-13 16:05:03.507][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-13 16:05:03.508][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-07-13 16:05:03.509][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-13 16:05:03.511][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-13 16:05:03.512][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2024-07-13 16:05:03.513][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2024-07-13 16:05:03.514][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-07-13 16:05:03.515][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-13 16:05:03.516][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-07-13 16:05:03.518][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-13 16:05:03.519][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-13 16:05:03.520][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2024-07-13 16:05:03.521][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-13 16:05:03.522][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2024-07-13 16:05:03.522][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2024-07-13 16:05:03.522][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2024-07-13 16:05:03.522][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2024-07-13 16:05:03.522][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2024-07-13 16:05:03.522][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2024-07-13 16:05:03.522][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2024-07-13 16:05:03.522][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2024-07-13 16:05:03.522][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2024-07-13 16:05:03.522][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2024-07-13 16:05:03.522][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2024-07-13 16:05:03.522][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2024-07-13 16:05:03.522][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2024-07-13 16:05:03.522][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2024-07-13 16:05:03.522][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2024-07-13 16:05:03.522][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2024-07-13 16:05:03.522][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2024-07-13 16:05:03.522][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2024-07-13 16:05:03.524][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-07-13 16:05:03.525][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-13 16:05:03.525][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2024-07-13 16:05:03.525][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2024-07-13 16:05:03.526][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-07-13 16:05:03.528][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-13 16:05:03.529][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-13 16:05:03.530][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-13 16:05:03.531][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-13 16:05:03.532][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-13 16:05:03.533][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-13 16:05:03.534][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2024-07-13 16:05:03.534][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2024-07-13 16:05:03.536][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-13 16:05:03.537][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-13 16:05:03.538][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-07-13 16:05:03.539][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:05:03.572][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2024-07-13 16:05:03.574][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-07-13 16:05:03.576][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-07-13 16:05:03.577][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-07-13 16:05:03.579][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-07-13 16:05:03.600][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2024-07-13 16:05:03.602][initialize] Register connector hmdb.metabolites with the request scheduler
biodb.DEBUG[2024-07-13 16:05:03.605][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites.
biodb.DEBUG[2024-07-13 16:05:03.609][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2024-07-13 16:05:03.613][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-07-13 16:05:03.614][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-07-13 16:05:03.616][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca".
biodb.DEBUG[2024-07-13 16:05:03.617][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.INFO [2024-07-13 16:05:03.626][biodb::testThat]
biodb.INFO [2024-07-13 16:05:03.627][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-07-13 16:05:03.629][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-13 16:05:03.630][biodb::testThat]
biodb.TRACE[2024-07-13 16:05:03.636][loadFileContents] Loaded 1 files from cache: [1]: "E:/biocbuild/bbs-3.19-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/testref/entry-hmdb.metabolites-HMDB0000001-content.xml".
biodb.DEBUG[2024-07-13 16:05:03.637][biodb$getFactory()$createEntryFromCo ...] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2024-07-13 16:05:03.641][biodb$getFactory()$createEntryFromCo ...] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2024-07-13 16:05:03.647][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-13 16:05:03.648][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:05:03.650][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:05:03.665][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:05:03.667][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:05:03.668][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:05:03.669][FUN] Functions in observer BiodbConfig: [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[2024-07-13 16:05:03.679][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:05:03.681][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:05:03.682][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:03.683][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:03.685][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:05:03.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:05:03.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:03.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:03.700][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-07-13 16:05:03.701][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-07-13 16:05:03.702][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:03.703][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:03.725][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-07-13 16:05:03.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-07-13 16:05:03.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:03.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:03.731][ef$get] Asked field names are: average.mass.
biodb.TRACE[2024-07-13 16:05:03.732][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-07-13 16:05:03.733][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:03.734][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:03.736][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-07-13 16:05:03.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-07-13 16:05:03.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:03.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:03.741][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-07-13 16:05:03.742][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-07-13 16:05:03.743][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:03.744][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:03.746][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-07-13 16:05:03.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-07-13 16:05:03.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:03.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:03.751][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-13 16:05:03.752][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-13 16:05:03.753][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:03.755][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:03.756][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-13 16:05:03.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-13 16:05:03.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:03.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:03.761][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-07-13 16:05:03.762][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-07-13 16:05:03.764][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:03.765][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:03.766][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-07-13 16:05:03.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-07-13 16:05:03.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:03.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:03.782][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-13 16:05:03.783][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-13 16:05:03.784][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:03.785][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:03.787][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-13 16:05:03.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-13 16:05:03.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:03.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:03.792][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-13 16:05:03.793][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-13 16:05:03.794][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:03.795][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:03.797][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-13 16:05:03.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-13 16:05:03.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:03.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:03.802][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-13 16:05:03.803][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-13 16:05:03.804][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:03.806][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:03.807][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-13 16:05:03.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-13 16:05:03.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:03.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:03.812][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-07-13 16:05:03.813][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-07-13 16:05:03.814][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:03.816][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:03.817][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-07-13 16:05:03.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-07-13 16:05:03.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:03.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:03.822][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-13 16:05:03.823][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-13 16:05:03.824][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:03.826][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:03.827][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-13 16:05:03.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-13 16:05:03.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:03.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:03.832][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-13 16:05:03.833][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-13 16:05:03.834][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:03.835][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:03.837][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-13 16:05:03.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-13 16:05:03.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:03.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:03.842][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-13 16:05:03.843][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-13 16:05:03.844][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:03.845][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:03.847][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-13 16:05:03.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-13 16:05:03.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:03.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:03.852][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-13 16:05:03.853][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-13 16:05:03.854][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:03.855][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:03.857][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-13 16:05:03.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-13 16:05:03.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:03.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:03.862][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:05:03.863][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:05:03.864][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:03.865][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:03.867][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:05:03.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:05:03.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:03.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:03.872][ef$get] Asked field names are: description.
biodb.TRACE[2024-07-13 16:05:03.873][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-07-13 16:05:03.874][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:03.875][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:03.877][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-07-13 16:05:03.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-07-13 16:05:03.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:03.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:03.882][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-13 16:05:03.883][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-13 16:05:03.884][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:03.885][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:03.887][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-13 16:05:03.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-13 16:05:03.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:03.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:03.891][ef$get] Asked field names are: super.class.
biodb.TRACE[2024-07-13 16:05:03.893][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-07-13 16:05:03.894][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:03.895][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:03.897][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2024-07-13 16:05:03.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-07-13 16:05:03.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:03.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:03.902][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:05:03.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:05:03.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:03.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:03.906][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:05:03.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:05:03.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:03.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:03.911][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:05:03.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:05:03.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:03.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:03.947][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-07-13 16:05:03.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-07-13 16:05:03.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:03.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:03.952][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-07-13 16:05:03.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-07-13 16:05:03.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:03.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:03.957][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-07-13 16:05:03.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-07-13 16:05:03.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:03.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:03.962][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-07-13 16:05:03.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-07-13 16:05:03.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:03.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:03.967][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-07-13 16:05:03.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-07-13 16:05:03.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:03.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:03.972][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-07-13 16:05:03.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-07-13 16:05:03.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:03.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:03.976][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-13 16:05:03.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-13 16:05:03.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:03.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:03.981][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-13 16:05:03.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-13 16:05:03.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:03.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:03.986][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-13 16:05:03.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-13 16:05:03.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:03.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:03.991][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-07-13 16:05:03.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-07-13 16:05:03.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:03.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:03.996][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-07-13 16:05:03.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-07-13 16:05:03.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:03.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.000][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-07-13 16:05:04.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-07-13 16:05:04.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.005][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-13 16:05:04.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-13 16:05:04.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.010][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-13 16:05:04.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-13 16:05:04.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.015][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-13 16:05:04.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-13 16:05:04.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.020][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-07-13 16:05:04.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-07-13 16:05:04.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.024][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-07-13 16:05:04.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-07-13 16:05:04.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.029][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-07-13 16:05:04.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-07-13 16:05:04.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.034][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-07-13 16:05:04.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-07-13 16:05:04.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.039][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-07-13 16:05:04.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-07-13 16:05:04.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.044][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-07-13 16:05:04.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-07-13 16:05:04.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.048][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-07-13 16:05:04.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-07-13 16:05:04.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.053][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-07-13 16:05:04.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-07-13 16:05:04.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.058][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-07-13 16:05:04.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-07-13 16:05:04.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.063][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-13 16:05:04.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-13 16:05:04.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.068][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-13 16:05:04.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-13 16:05:04.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.072][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-13 16:05:04.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-13 16:05:04.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.077][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-13 16:05:04.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-13 16:05:04.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.082][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-13 16:05:04.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-13 16:05:04.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.087][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-13 16:05:04.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-13 16:05:04.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.092][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-13 16:05:04.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-13 16:05:04.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.097][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-13 16:05:04.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-13 16:05:04.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.101][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-13 16:05:04.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-13 16:05:04.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.106][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-13 16:05:04.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-13 16:05:04.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.115][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-13 16:05:04.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-13 16:05:04.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.120][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-13 16:05:04.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-13 16:05:04.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.125][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-13 16:05:04.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-13 16:05:04.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.130][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-13 16:05:04.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-13 16:05:04.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.135][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-13 16:05:04.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-13 16:05:04.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.140][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:05:04.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:05:04.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.145][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:05:04.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:05:04.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.150][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:05:04.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:05:04.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.154][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-13 16:05:04.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-13 16:05:04.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.159][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-13 16:05:04.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-13 16:05:04.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.164][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-13 16:05:04.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-13 16:05:04.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.169][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-07-13 16:05:04.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-07-13 16:05:04.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.174][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-07-13 16:05:04.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-07-13 16:05:04.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.179][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-07-13 16:05:04.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-07-13 16:05:04.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.183][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-13 16:05:04.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-13 16:05:04.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.188][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-13 16:05:04.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-13 16:05:04.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.193][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-13 16:05:04.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-13 16:05:04.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.198][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2024-07-13 16:05:04.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-13 16:05:04.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.203][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-13 16:05:04.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-13 16:05:04.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.207][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-13 16:05:04.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-13 16:05:04.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.212][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-13 16:05:04.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-13 16:05:04.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.217][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2024-07-13 16:05:04.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-13 16:05:04.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.238][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:05:04.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:05:04.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.243][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:05:04.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:05:04.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.248][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:05:04.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:05:04.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.253][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:05:04.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:05:04.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.257][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:05:04.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:05:04.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.263][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-07-13 16:05:04.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-07-13 16:05:04.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.267][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-07-13 16:05:04.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-07-13 16:05:04.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.272][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:05:04.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:05:04.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.277][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-07-13 16:05:04.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-07-13 16:05:04.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.287][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:05:04.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:05:04.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.292][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:05:04.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:05:04.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.297][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:05:04.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:05:04.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.302][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:05:04.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:05:04.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.307][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:05:04.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:05:04.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.312][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:05:04.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:05:04.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-13 16:05:04.316][biodb$getFactory()$createEntryFromCo ...] Accession numbers: HMDB0000001.
biodb.TRACE[2024-07-13 16:05:04.320][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-13 16:05:04.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-13 16:05:04.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.324][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-13 16:05:04.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-13 16:05:04.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.329][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-07-13 16:05:04.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-07-13 16:05:04.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.334][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-07-13 16:05:04.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-07-13 16:05:04.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.359][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:05:04.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:05:04.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.377][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-07-13 16:05:04.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-07-13 16:05:04.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.388][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:05:04.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:05:04.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.393][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:05:04.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:05:04.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.398][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:05:04.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:05:04.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.405][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:05:04.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:05:04.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.410][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:05:04.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:05:04.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.414][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:05:04.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:05:04.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.419][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-07-13 16:05:04.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-07-13 16:05:04.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.424][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-07-13 16:05:04.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-07-13 16:05:04.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.429][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-07-13 16:05:04.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-07-13 16:05:04.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.446][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:05:04.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:05:04.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.451][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:05:04.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:05:04.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.456][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:05:04.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:05:04.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.460][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:05:04.462][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:05:04.463][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.464][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.465][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:05:04.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:05:04.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.486][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-07-13 16:05:04.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-07-13 16:05:04.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.492][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-07-13 16:05:04.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-07-13 16:05:04.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.496][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-07-13 16:05:04.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-07-13 16:05:04.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.516][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-07-13 16:05:04.517][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-07-13 16:05:04.519][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.520][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.521][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-07-13 16:05:04.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-07-13 16:05:04.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.536][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-07-13 16:05:04.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-07-13 16:05:04.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.541][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-07-13 16:05:04.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-07-13 16:05:04.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.546][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-07-13 16:05:04.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-07-13 16:05:04.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.551][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-07-13 16:05:04.552][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-07-13 16:05:04.554][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.555][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.556][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-07-13 16:05:04.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-07-13 16:05:04.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.571][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-13 16:05:04.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-13 16:05:04.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.576][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-13 16:05:04.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-13 16:05:04.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.581][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-13 16:05:04.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-13 16:05:04.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.586][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-13 16:05:04.587][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-13 16:05:04.588][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.589][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.590][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-13 16:05:04.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-13 16:05:04.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.605][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-13 16:05:04.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-13 16:05:04.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.610][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-13 16:05:04.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-13 16:05:04.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.615][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-13 16:05:04.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-13 16:05:04.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.620][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-13 16:05:04.621][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-13 16:05:04.622][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.623][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.624][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-13 16:05:04.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-13 16:05:04.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.639][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-13 16:05:04.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-13 16:05:04.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.644][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-13 16:05:04.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-13 16:05:04.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.649][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-13 16:05:04.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-13 16:05:04.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.654][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-13 16:05:04.655][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-13 16:05:04.656][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.658][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.659][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-13 16:05:04.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-13 16:05:04.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.679][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:05:04.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:05:04.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.684][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:05:04.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:05:04.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.689][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:05:04.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:05:04.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.693][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:05:04.695][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:05:04.696][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.697][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.698][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:05:04.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:05:04.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.713][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-07-13 16:05:04.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-07-13 16:05:04.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.718][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-07-13 16:05:04.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-07-13 16:05:04.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.723][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-07-13 16:05:04.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-07-13 16:05:04.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.728][ef$get] Asked field names are: description.
biodb.TRACE[2024-07-13 16:05:04.729][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-07-13 16:05:04.730][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.731][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.733][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-07-13 16:05:04.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-07-13 16:05:04.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.747][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-13 16:05:04.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-13 16:05:04.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.752][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-13 16:05:04.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-13 16:05:04.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.757][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-13 16:05:04.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-13 16:05:04.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.762][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-13 16:05:04.763][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-13 16:05:04.765][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.766][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.767][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-13 16:05:04.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-13 16:05:04.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.782][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-07-13 16:05:04.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-07-13 16:05:04.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.787][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-07-13 16:05:04.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-07-13 16:05:04.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.792][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-07-13 16:05:04.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-07-13 16:05:04.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.796][ef$get] Asked field names are: average.mass.
biodb.TRACE[2024-07-13 16:05:04.798][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-07-13 16:05:04.799][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.800][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.801][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-07-13 16:05:04.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-07-13 16:05:04.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.816][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-13 16:05:04.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-13 16:05:04.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.821][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-13 16:05:04.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-13 16:05:04.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.826][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-13 16:05:04.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-13 16:05:04.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.830][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-13 16:05:04.832][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-13 16:05:04.833][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.834][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.835][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-13 16:05:04.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-13 16:05:04.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.850][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-07-13 16:05:04.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-07-13 16:05:04.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.855][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-07-13 16:05:04.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-07-13 16:05:04.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.865][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-07-13 16:05:04.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-07-13 16:05:04.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.870][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-07-13 16:05:04.871][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-07-13 16:05:04.872][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.873][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.874][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-07-13 16:05:04.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-07-13 16:05:04.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.889][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-13 16:05:04.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-13 16:05:04.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.894][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-13 16:05:04.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-13 16:05:04.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.899][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-13 16:05:04.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-13 16:05:04.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.904][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-13 16:05:04.905][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-13 16:05:04.906][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.907][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.909][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-13 16:05:04.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-13 16:05:04.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.923][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-07-13 16:05:04.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-07-13 16:05:04.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.928][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-07-13 16:05:04.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-07-13 16:05:04.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.933][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-07-13 16:05:04.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-07-13 16:05:04.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.938][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-07-13 16:05:04.939][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-07-13 16:05:04.940][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.941][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.942][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-07-13 16:05:04.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-07-13 16:05:04.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.957][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-13 16:05:04.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-13 16:05:04.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.962][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-13 16:05:04.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-13 16:05:04.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.967][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-13 16:05:04.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-13 16:05:04.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.971][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-13 16:05:04.973][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-13 16:05:04.974][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.975][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.976][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-13 16:05:04.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-13 16:05:04.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.990][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-13 16:05:04.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-13 16:05:04.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:04.996][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-13 16:05:04.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-13 16:05:04.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:04.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:05.000][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-13 16:05:05.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-13 16:05:05.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:05.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:05.005][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-13 16:05:05.006][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-13 16:05:05.008][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:05.009][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:05.010][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-13 16:05:05.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-13 16:05:05.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:05.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:05.024][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-13 16:05:05.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-13 16:05:05.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:05.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:05.029][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-13 16:05:05.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-13 16:05:05.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:05.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:05.034][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-13 16:05:05.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-13 16:05:05.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:05.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:05.044][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-13 16:05:05.045][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-13 16:05:05.046][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:05.047][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:05.049][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-13 16:05:05.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-13 16:05:05.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:05.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:05.063][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-07-13 16:05:05.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-07-13 16:05:05.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:05.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:05.068][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-07-13 16:05:05.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-07-13 16:05:05.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:05.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:05.073][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-07-13 16:05:05.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-07-13 16:05:05.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:05.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:05.078][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-07-13 16:05:05.079][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-07-13 16:05:05.080][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:05.082][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:05.083][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-07-13 16:05:05.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-07-13 16:05:05.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:05.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:05.097][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:05:05.099][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:05:05.100][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:05.101][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:05.108][ef$get] Asked field names are: average.mass.
biodb.TRACE[2024-07-13 16:05:05.109][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-07-13 16:05:05.111][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:05.112][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:05.118][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-07-13 16:05:05.119][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-07-13 16:05:05.121][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:05.122][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:05.128][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-13 16:05:05.130][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-13 16:05:05.131][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:05.132][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:05.138][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-07-13 16:05:05.140][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-07-13 16:05:05.141][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:05.142][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:05.149][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-13 16:05:05.150][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-13 16:05:05.151][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:05.152][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:05.159][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-07-13 16:05:05.160][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-07-13 16:05:05.161][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:05.162][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:05.169][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-07-13 16:05:05.170][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-07-13 16:05:05.172][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:05.173][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:05.179][ef$get] Asked field names are: description.
biodb.TRACE[2024-07-13 16:05:05.181][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-07-13 16:05:05.182][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:05.183][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:05.190][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-13 16:05:05.191][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-13 16:05:05.192][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:05.193][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:05.200][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-13 16:05:05.201][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-13 16:05:05.202][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:05.203][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:05.210][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-13 16:05:05.211][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-13 16:05:05.213][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:05.214][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:05.220][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-13 16:05:05.222][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-13 16:05:05.223][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:05.224][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:05.230][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-13 16:05:05.232][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-13 16:05:05.233][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:05.234][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:05.246][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:05:05.247][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:05:05.249][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:05.250][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:05.256][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-13 16:05:05.258][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-13 16:05:05.259][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:05.260][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:05.267][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-07-13 16:05:05.268][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-07-13 16:05:05.269][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:05.270][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:05:05.277][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-13 16:05:05.279][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-13 16:05:05.280][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:05.281][ef$get] fields variable is a list.
biodb.INFO [2024-07-13 16:05:05.293][biodb::testThat]
biodb.INFO [2024-07-13 16:05:05.294][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-07-13 16:05:05.296][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-13 16:05:05.297][biodb::testThat]
biodb.DEBUG[2024-07-13 16:05:05.310][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2024-07-13 16:05:05.316][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.INFO [2024-07-13 16:05:05.322][self$getFolderPath] Create cache folder "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34" for "hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34".
biodb.DEBUG[2024-07-13 16:05:05.324][self$isDownloaded] Database hmdb.metabolites has not yet been downloaded.
biodb.INFO [2024-07-13 16:05:05.325][self$download] Downloading whole database of hmdb.metabolites.
biodb.INFO [2024-07-13 16:05:05.326][private$doDownload] Downloading HMDB metabolite database at "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip" ...
biodb.DEBUG[2024-07-13 16:05:05.329][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 25.6 MB

biodb.INFO [2024-07-13 16:05:22.350][biodb::testThat]
biodb.INFO [2024-07-13 16:05:22.351][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-07-13 16:05:22.352][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-13 16:05:22.354][biodb::testThat]
biodb.TRACE[2024-07-13 16:05:22.357][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:05:22.359][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:05:22.360][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:05:22.361][ef$get] fields variable is a list.
biodb.DEBUG[2024-07-13 16:05:22.363][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "name".
biodb.DEBUG[2024-07-13 16:05:22.393][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2024-07-13 16:05:22.432][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2024-07-13 16:05:22.435][self$isDownloaded] Database hmdb.metabolites has not yet been downloaded.
biodb.INFO [2024-07-13 16:05:22.436][self$download] Downloading whole database of hmdb.metabolites.
biodb.INFO [2024-07-13 16:05:22.437][private$doDownload] Downloading HMDB metabolite database at "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip" ...
biodb.DEBUG[2024-07-13 16:05:22.451][sched$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 34.2 MB

biodb.INFO [2024-07-13 16:06:09.019][biodb::testThat]
biodb.INFO [2024-07-13 16:06:09.021][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-07-13 16:06:09.022][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-13 16:06:09.023][biodb::testThat]
biodb.DEBUG[2024-07-13 16:06:09.033][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2024-07-13 16:06:09.035][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2024-07-13 16:06:09.037][self$isDownloaded] Database hmdb.metabolites has not yet been downloaded.
biodb.INFO [2024-07-13 16:06:09.038][self$download] Downloading whole database of hmdb.metabolites.
biodb.INFO [2024-07-13 16:06:09.040][private$doDownload] Downloading HMDB metabolite database at "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip" ...
biodb.DEBUG[2024-07-13 16:06:09.042][sched$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 115.6 MB

biodb.INFO [2024-07-13 16:06:58.699][biodb::testThat]
biodb.INFO [2024-07-13 16:06:58.701][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-07-13 16:06:58.702][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-13 16:06:58.703][biodb::testThat]
biodb.DEBUG[2024-07-13 16:06:58.708][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2024-07-13 16:06:58.710][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2024-07-13 16:06:58.712][self$isDownloaded] Database hmdb.metabolites has not yet been downloaded.
biodb.INFO [2024-07-13 16:06:58.713][self$download] Downloading whole database of hmdb.metabolites.
biodb.INFO [2024-07-13 16:06:58.715][private$doDownload] Downloading HMDB metabolite database at "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip" ...
biodb.DEBUG[2024-07-13 16:06:58.718][sched$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 130.8 MB

biodb.INFO [2024-07-13 16:08:14.693][biodb::testThat]
biodb.INFO [2024-07-13 16:08:14.695][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-07-13 16:08:14.696][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-13 16:08:14.697][biodb::testThat]
biodb.INFO [2024-07-13 16:08:14.709][biodb::testThat]
biodb.INFO [2024-07-13 16:08:14.710][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-07-13 16:08:14.711][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-13 16:08:14.712][biodb::testThat]
biodb.INFO [2024-07-13 16:08:14.723][biodb::testThat]
biodb.INFO [2024-07-13 16:08:14.724][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-07-13 16:08:14.725][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-13 16:08:14.726][biodb::testThat]
biodb.DEBUG[2024-07-13 16:08:14.731][function(conn, opt)] Trying to download "http://www.hmdb.ca/metabolites/HMDB0000001".
biodb.DEBUG[2024-07-13 16:08:15.022][getUrlContent] Use base::url() for downloading content of URL http://www.hmdb.ca/metabolites/HMDB0000001.
biodb.INFO [2024-07-13 16:08:35.481][biodb::testThat]
biodb.INFO [2024-07-13 16:08:35.484][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-07-13 16:08:35.485][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-13 16:08:35.487][biodb::testThat]
biodb.DEBUG[2024-07-13 16:08:35.663][getUrlContent] Use base::url() for downloading content of URL http://www.hmdb.ca/structures/HMDB0000001/image.png.
biodb.TRACE[2024-07-13 16:08:41.510][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:08:41.512][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:08:41.514][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:08:41.515][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:08:41.516][ef$get] Asked field names are: description.
biodb.TRACE[2024-07-13 16:08:41.518][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-07-13 16:08:41.519][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:08:41.520][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:08:41.522][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-07-13 16:08:41.523][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-07-13 16:08:41.524][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:08:41.526][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:08:41.527][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:08:41.529][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:08:41.530][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:08:41.531][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:08:41.533][ef$get] Asked field names are: description.
biodb.TRACE[2024-07-13 16:08:41.534][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-07-13 16:08:41.535][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:08:41.536][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:08:41.538][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-07-13 16:08:41.539][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-07-13 16:08:41.540][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:08:41.541][ef$get] fields variable is a list.
biodb.INFO [2024-07-13 16:08:41.543][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-07-13 16:08:41.545][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler
biodb.INFO [2024-07-13 16:08:41.546][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2024-07-13 16:08:41.547][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-07-13 16:08:41.548][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:08:41.550][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:08:41.551][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:08:41.552][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:08:41.553][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:08:41.555][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 4 | WARN 8 | SKIP 0 | PASS 113 ]

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

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

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbHmdb_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbuild/bbs-3.19-bioc-longtests/meat/biodbHmdb.Rcheck'
* using R version 4.4.1 (2024-06-14 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* 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 '1.10.0'
* 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 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 'E:/biocbuild/bbs-3.19-bioc-longtests/meat/biodbHmdb.Rcheck/00install.out' for details.
* used C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: 'zip'
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  'HmdbMetabolitesConn' 'HmdbMetabolitesEntry' 'hmdbToSqlite'
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking files in 'vignettes' ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in 'longtests' ... OK
* checking tests in 'longtests' ...
  Running 'testthat.R'
 ERROR
Running the tests in 'longtests/testthat.R' failed.
Last 13 lines of output:
    1. ├─base::do.call(fct, params)
    2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
    3.   └─opt$refEntries$getRealEntry(id)
    4.     └─self$getRealEntries(ids = id)
    5.       └─private$bdb$getFactory()$getEntry(...)
    6.         └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
    7.           └─conn$getEntryContent(ids)
    8.             └─self$download()
    9.               └─private$doDownload()
   10.                 └─sched$downloadFile(url = zip.url, dest.file = tmpFile)
   11.                   └─utils::download.file(...)
  
  [ FAIL 4 | WARN 8 | SKIP 0 | PASS 113 ]
  Error: Test failures
  Execution halted
* DONE

Status: 1 ERROR, 2 WARNINGs, 1 NOTE
See
  'E:/biocbuild/bbs-3.19-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__~1.EXE (GCC) 13.2.0'
g++ -std=gnu++17  -I"E:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.19-bioc/R/library/testthat/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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"E:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.19-bioc/R/library/testthat/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c FileEntryMaker.cpp -o FileEntryMaker.o
g++ -std=gnu++17  -I"E:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.19-bioc/R/library/testthat/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17  -I"E:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.19-bioc/R/library/testthat/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c StringEnrtryMaker.cpp -o StringEnrtryMaker.o
g++ -std=gnu++17  -I"E:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.19-bioc/R/library/testthat/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c TagDetector.cpp -o TagDetector.o
g++ -std=gnu++17  -I"E:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.19-bioc/R/library/testthat/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c XmlSplitter.cpp -o XmlSplitter.o
g++ -std=gnu++17  -I"E:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.19-bioc/R/library/testthat/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c extractXmlEntries.cpp -o extractXmlEntries.o
g++ -std=gnu++17  -I"E:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.19-bioc/R/library/testthat/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c test-100-TagDetector.cpp -o test-100-TagDetector.o
g++ -std=gnu++17  -I"E:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.19-bioc/R/library/testthat/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c test-150-StringEntryMaker.cpp -o test-150-StringEntryMaker.o
g++ -std=gnu++17  -I"E:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.19-bioc/R/library/testthat/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c test-200-XmlSplitter.cpp -o test-200-XmlSplitter.o
g++ -std=gnu++17  -I"E:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.19-bioc/R/library/testthat/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c test-runner.cpp -o test-runner.o
g++ -std=gnu++17 -shared -s -static-libgcc -o biodbHmdb.dll tmp.def 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 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LE:/biocbuild/bbs-3.19-bioc/R/bin/x64 -lR
installing to E:/biocbuild/bbs-3.19-bioc-longtests/meat/biodbHmdb.Rcheck/00LOCK-biodbHmdb/00new/biodbHmdb/libs/x64
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (biodbHmdb)