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 7/33HostnameOS / ArchCHECK
biodbExpasy 1.8.0  (landing page)
Pierrick Roger
Snapshot Date: 2024-07-13 09:55 -0400 (Sat, 13 Jul 2024)
git_url: https://git.bioconductor.org/packages/biodbExpasy
git_branch: RELEASE_3_19
git_last_commit: de004e8
git_last_commit_date: 2024-04-30 11:41:12 -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 biodbExpasy on palomino7

To the developers/maintainers of the biodbExpasy 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: biodbExpasy
Version: 1.8.0
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 biodbExpasy_1.8.0.tar.gz
StartedAt: 2024-07-13 16:03:28 -0400 (Sat, 13 Jul 2024)
EndedAt: 2024-07-13 16:04:16 -0400 (Sat, 13 Jul 2024)
EllapsedTime: 48.1 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbExpasy.Rcheck
Warnings: NA

Tests output

biodbExpasy.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(biodbExpasy)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbExpasy")
biodb.INFO [2024-07-13 16:04:08.834][biodb::testContext]
biodb.INFO [2024-07-13 16:04:08.837][biodb::testContext] ********************************************************************************
biodb.INFO [2024-07-13 16:04:08.839][biodb::testContext] Test context - Generic long tests
biodb.INFO [2024-07-13 16:04:08.840][biodb::testContext] ********************************************************************************
biodb.INFO [2024-07-13 16:04:08.841][biodb::testContext]
biodb.INFO [2024-07-13 16:04:08.849][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-07-13 16:04:08.852][self$loadDefinitions] Load definitions from file "E:/biocbuild/bbs-3.19-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2024-07-13 16:04:08.885][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-13 16:04:08.887][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-07-13 16:04:08.888][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-07-13 16:04:08.889][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:08.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:08.892][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:04:08.893][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-07-13 16:04:08.924][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-07-13 16:04:08.926][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:08.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:08.928][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:04:08.929][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-07-13 16:04:08.930][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-07-13 16:04:08.931][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:08.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:08.934][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:04:08.935][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-07-13 16:04:08.936][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-07-13 16:04:08.937][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-07-13 16:04:08.938][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:08.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:08.941][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:04:08.942][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-07-13 16:04:08.943][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-07-13 16:04:08.944][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-07-13 16:04:08.945][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:08.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:08.947][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:04:08.949][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-07-13 16:04:08.950][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-07-13 16:04:08.951][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:08.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:08.953][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:04:08.954][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-07-13 16:04:08.956][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-07-13 16:04:08.957][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-07-13 16:04:08.958][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:08.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:08.960][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:04:08.961][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-07-13 16:04:08.962][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-07-13 16:04:08.964][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:08.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:08.966][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:04:08.967][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-07-13 16:04:08.968][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-07-13 16:04:08.969][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-07-13 16:04:08.970][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:08.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:08.972][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:04:08.974][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-07-13 16:04:08.975][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-07-13 16:04:08.976][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-07-13 16:04:08.977][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-07-13 16:04:08.979][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-07-13 16:04:08.980][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-07-13 16:04:08.981][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:08.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:08.983][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:04:08.984][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-07-13 16:04:08.985][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-07-13 16:04:08.987][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:08.988][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:08.989][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:04:08.990][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-07-13 16:04:08.991][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-07-13 16:04:08.992][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:08.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:08.994][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:04:08.995][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-07-13 16:04:08.997][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-07-13 16:04:08.998][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:08.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:09.000][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:04:09.001][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-07-13 16:04:09.002][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-07-13 16:04:09.003][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:09.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:09.006][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:04:09.007][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-07-13 16:04:09.008][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-07-13 16:04:09.009][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:09.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:09.011][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:04:09.012][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-07-13 16:04:09.013][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-07-13 16:04:09.017][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-07-13 16:04:09.018][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:09.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:09.021][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:04:09.022][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-07-13 16:04:09.023][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-07-13 16:04:09.024][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-07-13 16:04:09.025][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:09.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:09.027][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:04:09.030][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-07-13 16:04:09.057][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-13 16:04:09.071][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-07-13 16:04:09.072][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-13 16:04:09.074][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-13 16:04:09.075][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-13 16:04:09.076][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-13 16:04:09.077][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-13 16:04:09.079][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-13 16:04:09.080][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-13 16:04:09.081][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-13 16:04:09.082][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-13 16:04:09.083][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-07-13 16:04:09.085][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-13 16:04:09.086][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:04:09.087][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-13 16:04:09.088][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-13 16:04:09.088][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-13 16:04:09.088][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-13 16:04:09.088][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-07-13 16:04:09.088][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-07-13 16:04:09.090][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-13 16:04:09.091][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-13 16:04:09.092][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-13 16:04:09.093][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-13 16:04:09.094][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-13 16:04:09.096][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-13 16:04:09.097][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-13 16:04:09.103][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:04:09.105][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-13 16:04:09.106][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-13 16:04:09.107][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-13 16:04:09.108][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:04:09.109][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-07-13 16:04:09.111][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-13 16:04:09.112][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-07-13 16:04:09.114][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-13 16:04:09.115][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-13 16:04:09.116][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-13 16:04:09.117][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-13 16:04:09.118][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-13 16:04:09.119][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-13 16:04:09.121][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-07-13 16:04:09.122][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-13 16:04:09.123][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-13 16:04:09.124][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-07-13 16:04:09.125][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-13 16:04:09.127][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:04:09.128][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-13 16:04:09.129][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-13 16:04:09.129][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-13 16:04:09.129][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-13 16:04:09.129][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-07-13 16:04:09.129][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-07-13 16:04:09.130][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-13 16:04:09.131][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-13 16:04:09.132][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-13 16:04:09.133][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-13 16:04:09.135][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-13 16:04:09.136][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-13 16:04:09.137][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-13 16:04:09.138][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:04:09.139][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-13 16:04:09.140][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-13 16:04:09.141][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-13 16:04:09.143][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:04:09.144][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-07-13 16:04:09.146][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-07-13 16:04:09.147][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-07-13 16:04:09.148][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-13 16:04:09.150][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-13 16:04:09.151][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-13 16:04:09.152][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-13 16:04:09.153][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-13 16:04:09.154][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-13 16:04:09.156][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-13 16:04:09.157][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-13 16:04:09.158][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-07-13 16:04:09.159][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-07-13 16:04:09.160][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-13 16:04:09.161][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:04:09.163][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-13 16:04:09.164][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:04:09.165][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-13 16:04:09.166][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-13 16:04:09.167][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-13 16:04:09.168][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-13 16:04:09.170][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-13 16:04:09.171][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-13 16:04:09.172][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-13 16:04:09.173][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:04:09.174][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-13 16:04:09.175][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-13 16:04:09.176][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-13 16:04:09.178][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:04:09.179][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-07-13 16:04:09.181][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-07-13 16:04:09.182][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-07-13 16:04:09.183][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-13 16:04:09.185][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-13 16:04:09.186][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-13 16:04:09.187][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-13 16:04:09.188][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-13 16:04:09.189][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-13 16:04:09.190][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-07-13 16:04:09.192][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-13 16:04:09.193][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-07-13 16:04:09.194][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-07-13 16:04:09.195][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-13 16:04:09.196][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:04:09.198][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-13 16:04:09.199][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:04:09.200][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-13 16:04:09.201][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-13 16:04:09.202][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-13 16:04:09.203][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-13 16:04:09.205][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-13 16:04:09.206][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-13 16:04:09.207][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-13 16:04:09.208][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:04:09.209][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-13 16:04:09.210][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-13 16:04:09.211][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-13 16:04:09.212][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:04:09.216][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-13 16:04:09.217][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:09.218][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:04:09.219][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:09.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:09.221][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 16:04:09.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:09.223][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:04:09.225][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:09.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:09.227][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 16:04:09.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:09.229][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:04:09.230][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:09.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:09.232][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 16:04:09.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:09.234][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:04:09.235][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:09.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:09.237][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 16:04:09.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:09.239][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:04:09.240][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:09.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:09.243][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 16:04:09.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:09.245][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:04:09.246][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:09.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:09.248][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 16:04:09.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:09.250][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:04:09.251][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:09.252][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:09.253][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 16:04:09.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:09.255][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:04:09.256][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:09.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:09.259][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 16:04:09.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:09.261][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:04:09.262][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:09.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:09.264][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 16:04:09.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:09.266][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:04:09.267][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:09.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:09.269][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 16:04:09.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:09.271][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:04:09.272][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:09.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:09.275][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 16:04:09.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:09.277][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:04:09.278][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:09.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:09.280][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 16:04:09.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:09.282][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:04:09.283][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:09.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:09.285][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 16:04:09.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:09.287][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:04:09.288][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:09.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:09.290][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 16:04:09.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:09.293][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:04:09.294][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:09.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:09.296][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 16:04:09.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:09.298][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:04:09.299][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:09.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:09.301][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 16:04:09.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:09.303][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:04:09.304][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:09.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:09.306][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 16:04:09.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:09.309][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:04:09.310][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-07-13 16:04:09.319][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-07-13 16:04:09.320][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-07-13 16:04:09.322][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-07-13 16:04:09.324][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-07-13 16:04:09.325][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-07-13 16:04:09.327][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-07-13 16:04:09.328][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-07-13 16:04:09.330][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-07-13 16:04:09.331][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-07-13 16:04:09.333][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-07-13 16:04:09.334][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-07-13 16:04:09.336][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-07-13 16:04:09.337][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-07-13 16:04:09.339][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-07-13 16:04:09.340][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-07-13 16:04:09.342][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-07-13 16:04:09.343][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-07-13 16:04:09.345][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-07-13 16:04:09.346][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-07-13 16:04:09.348][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-07-13 16:04:09.349][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-07-13 16:04:09.351][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-07-13 16:04:09.353][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-07-13 16:04:09.354][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-07-13 16:04:09.356][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-07-13 16:04:09.357][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-07-13 16:04:09.359][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-07-13 16:04:09.360][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-07-13 16:04:09.362][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-07-13 16:04:09.363][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-07-13 16:04:09.365][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-07-13 16:04:09.367][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-07-13 16:04:09.368][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-07-13 16:04:09.370][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-07-13 16:04:09.371][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-07-13 16:04:09.373][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-07-13 16:04:09.374][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-07-13 16:04:09.376][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-07-13 16:04:09.377][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-07-13 16:04:09.379][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-07-13 16:04:09.380][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-07-13 16:04:09.382][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-07-13 16:04:09.383][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-07-13 16:04:09.385][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-07-13 16:04:09.387][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-07-13 16:04:09.388][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-07-13 16:04:09.390][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-07-13 16:04:09.391][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-07-13 16:04:09.393][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-07-13 16:04:09.394][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-07-13 16:04:09.396][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-07-13 16:04:09.397][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-07-13 16:04:09.399][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-07-13 16:04:09.400][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-07-13 16:04:09.402][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-07-13 16:04:09.403][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-07-13 16:04:09.405][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-07-13 16:04:09.406][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-07-13 16:04:09.408][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-07-13 16:04:09.410][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-07-13 16:04:09.411][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-07-13 16:04:09.413][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-07-13 16:04:09.414][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-07-13 16:04:09.416][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-07-13 16:04:09.417][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-07-13 16:04:09.419][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-07-13 16:04:09.420][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-07-13 16:04:09.422][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-07-13 16:04:09.423][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-07-13 16:04:09.425][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-07-13 16:04:09.426][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-07-13 16:04:09.428][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-07-13 16:04:09.429][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-07-13 16:04:09.431][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-07-13 16:04:09.433][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-07-13 16:04:09.435][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-07-13 16:04:09.437][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-07-13 16:04:09.439][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-07-13 16:04:09.440][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-07-13 16:04:09.442][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-07-13 16:04:09.444][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-07-13 16:04:09.445][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-07-13 16:04:09.477][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-07-13 16:04:09.480][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-07-13 16:04:09.483][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-13 16:04:09.484][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:09.485][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 16:04:09.486][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:09.487][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:04:09.492][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:09.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:04:09.494][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:04:09.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:09.496][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:04:09.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:09.498][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:04:09.499][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:09.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:04:09.502][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:04:09.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:09.504][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:04:09.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:09.506][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:04:09.507][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:09.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:04:09.509][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:04:09.510][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:09.511][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 16:04:09.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:09.513][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:04:09.515][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:09.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:04:09.517][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:04:09.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:09.519][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 16:04:09.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:09.521][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:04:09.522][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:09.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:04:09.524][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:04:09.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:09.526][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 16:04:09.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:09.529][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:04:09.530][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:09.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:04:09.532][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:04:09.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:09.540][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 16:04:09.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:09.542][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:04:09.543][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:09.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:04:09.545][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:04:09.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:09.547][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:04:09.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:09.549][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:04:09.551][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:09.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:04:09.553][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:04:09.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:09.555][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 16:04:09.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:09.557][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:04:09.558][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:09.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:04:09.560][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:04:09.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:09.562][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 16:04:09.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:09.565][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:04:09.566][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:09.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:04:09.568][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:04:09.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:09.570][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 16:04:09.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:09.572][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:04:09.573][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:09.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:04:09.575][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:04:09.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:09.577][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 16:04:09.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:09.580][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:04:09.581][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:09.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:04:09.583][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:04:09.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:09.585][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 16:04:09.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:09.587][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:04:09.588][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:09.589][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:04:09.591][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:04:09.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:09.593][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 16:04:09.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:09.595][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:04:09.596][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:09.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:04:09.598][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:04:09.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:09.600][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 16:04:09.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:09.602][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:04:09.603][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:09.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:04:09.606][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:04:09.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:09.608][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 16:04:09.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:09.610][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:04:09.611][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:09.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:04:09.613][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:04:09.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:09.615][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 16:04:09.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:09.617][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:04:09.618][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:09.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:04:09.621][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:04:09.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:09.623][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 16:04:09.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:09.625][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:04:09.628][biodb$loadDefinitions] Load definitions from file "E:/biocbuild/bbs-3.19-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/definitions.yml".
biodb.DEBUG[2024-07-13 16:04:09.637][self$getDbsInfo()$define] Define connector expasy.enzyme.
biodb.DEBUG[2024-07-13 16:04:09.639][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-13 16:04:09.640][self$setPropertyValue] Setting property "description" to "Write here the description of this database.".
biodb.DEBUG[2024-07-13 16:04:09.642][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-13 16:04:09.643][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-13 16:04:09.644][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-13 16:04:09.645][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-13 16:04:09.646][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-07-13 16:04:09.648][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-13 16:04:09.649][self$setPropertyValue] Setting property "entry.content.type" to "txt".
biodb.DEBUG[2024-07-13 16:04:09.650][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-13 16:04:09.651][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-13 16:04:09.652][self$setPropertyValue] Setting property "name" to "Expasy ENZYME database.".
biodb.DEBUG[2024-07-13 16:04:09.654][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-13 16:04:09.655][self$setPropertyValue] Setting property "parsing.expr" to "^ID\s+([0-9.]+)$".
biodb.DEBUG[2024-07-13 16:04:09.655][self$setPropertyValue] Setting property "parsing.expr" to "^CA\s+(.+?)\.?$".
biodb.DEBUG[2024-07-13 16:04:09.655][self$setPropertyValue] Setting property "parsing.expr" to "^CF\s+(.+?)\.?$".
biodb.DEBUG[2024-07-13 16:04:09.655][self$setPropertyValue] Setting property "parsing.expr" to "^DE\s+(.+?)\.?$".
biodb.DEBUG[2024-07-13 16:04:09.656][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-07-13 16:04:09.657][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-13 16:04:09.658][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-07-13 16:04:09.660][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-13 16:04:09.661][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-13 16:04:09.662][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-13 16:04:09.663][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-13 16:04:09.664][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-13 16:04:09.665][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-13 16:04:09.666][self$setPropertyValue] Setting property "urls" to "https://enzyme.expasy.org/".
biodb.DEBUG[2024-07-13 16:04:09.668][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-13 16:04:09.669][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-13 16:04:09.670][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-07-13 16:04:09.671][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:04:09.677][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-07-13 16:04:09.698][super$initialize] Initialize connector expasy.enzyme.
biodb.DEBUG[2024-07-13 16:04:09.699][super$initialize] Register connector expasy.enzyme with the request scheduler
biodb.DEBUG[2024-07-13 16:04:09.703][private$bdb$getRequestScheduler()$re ...] Register connector expasy.enzyme.
biodb.DEBUG[2024-07-13 16:04:09.706][private$addConnectorRules] Create new rule for URL "enzyme.expasy.org" of connector "expasy.enzyme".
biodb.DEBUG[2024-07-13 16:04:09.710][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-07-13 16:04:09.711][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-07-13 16:04:09.712][biodb$getFactory()$createConn] Creating new connector expasy.enzyme for database class expasy.enzyme .
biodb.INFO [2024-07-13 16:04:09.722][biodb::testThat]
biodb.INFO [2024-07-13 16:04:09.723][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-07-13 16:04:09.724][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-13 16:04:09.726][biodb::testThat]
biodb.TRACE[2024-07-13 16:04:09.732][loadFileContents] Loaded 1 files from cache: [1]: "E:/biocbuild/bbs-3.19-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/testref/entry-expasy.enzyme-1.1.1.1-content.txt".
biodb.DEBUG[2024-07-13 16:04:09.734][biodb$getFactory()$createEntryFromCo ...] Creating Expasy ENZYME database. entries from 1 content(s).
biodb.DEBUG[2024-07-13 16:04:09.738][biodb$getFactory()$createEntryFromCo ...] Parsing 1 Expasy ENZYME database. entries.
biodb.DEBUG[2024-07-13 16:04:09.757][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-13 16:04:09.767][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:04:09.768][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:04:09.811][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:09.813][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 16:04:09.814][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:09.815][FUN] Functions in observer BiodbConfig: [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 16:04:09.824][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:04:09.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:04:09.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:09.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:09.850][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-07-13 16:04:09.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-07-13 16:04:09.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:09.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:09.865][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-07-13 16:04:09.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-07-13 16:04:09.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:09.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:09.871][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:04:09.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:04:09.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:09.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:09.876][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-07-13 16:04:09.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-07-13 16:04:09.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:09.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:09.881][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-07-13 16:04:09.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-07-13 16:04:09.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:09.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:09.885][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-07-13 16:04:09.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-07-13 16:04:09.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:09.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:09.890][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-07-13 16:04:09.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-07-13 16:04:09.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:09.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:09.895][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-07-13 16:04:09.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-07-13 16:04:09.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:09.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:09.915][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:04:09.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:04:09.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:09.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:09.920][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:04:09.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:04:09.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:09.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:09.989][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:04:09.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:04:09.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:09.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:09.994][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:04:09.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:04:09.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:09.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:09.999][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:04:10.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:04:10.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:10.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:10.004][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-07-13 16:04:10.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-07-13 16:04:10.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:10.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:10.009][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-07-13 16:04:10.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-07-13 16:04:10.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:10.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:10.014][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:04:10.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:04:10.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:10.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:10.019][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-07-13 16:04:10.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-07-13 16:04:10.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:10.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:10.024][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:04:10.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:04:10.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:10.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:10.029][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:04:10.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:04:10.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:10.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:10.033][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:04:10.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:04:10.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:10.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:10.038][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:04:10.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:04:10.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:10.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:10.043][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:04:10.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:04:10.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:10.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:10.048][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:04:10.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:04:10.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:10.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-13 16:04:10.053][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 1.1.1.1.
biodb.TRACE[2024-07-13 16:04:10.056][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-13 16:04:10.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-13 16:04:10.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:10.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:10.061][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-13 16:04:10.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-13 16:04:10.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:10.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:10.066][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-07-13 16:04:10.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-07-13 16:04:10.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:10.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:10.071][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-07-13 16:04:10.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-07-13 16:04:10.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:10.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:10.096][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:04:10.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:04:10.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:10.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:10.114][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-07-13 16:04:10.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-07-13 16:04:10.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:10.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:10.126][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:04:10.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:04:10.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:10.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:10.131][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:04:10.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:04:10.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:10.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:10.141][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:04:10.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:04:10.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:10.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:10.147][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:04:10.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:04:10.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:10.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:10.152][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:04:10.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:04:10.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:10.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:10.157][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:04:10.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:04:10.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:10.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:10.162][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-07-13 16:04:10.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-07-13 16:04:10.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:10.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:10.167][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-07-13 16:04:10.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-07-13 16:04:10.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:10.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:10.172][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-07-13 16:04:10.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-07-13 16:04:10.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:10.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:10.188][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:04:10.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:04:10.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:10.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:10.194][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:04:10.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:04:10.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:10.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:10.200][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:04:10.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:04:10.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:10.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:10.205][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:04:10.206][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:04:10.207][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:10.209][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:10.210][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:04:10.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:04:10.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:10.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:10.233][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:04:10.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:04:10.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:10.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:10.241][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:04:10.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:04:10.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:10.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:10.246][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:04:10.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:04:10.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:10.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:10.251][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:04:10.252][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:04:10.253][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:10.255][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:10.256][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:04:10.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:04:10.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:10.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:10.271][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-07-13 16:04:10.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-07-13 16:04:10.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:10.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:10.276][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-07-13 16:04:10.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-07-13 16:04:10.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:10.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:10.281][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-07-13 16:04:10.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-07-13 16:04:10.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:10.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:10.285][ef$get] Asked field names are: cofactor.
biodb.TRACE[2024-07-13 16:04:10.287][ef$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-07-13 16:04:10.288][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:10.289][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:10.290][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-07-13 16:04:10.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-07-13 16:04:10.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:10.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:10.305][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-07-13 16:04:10.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-07-13 16:04:10.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:10.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:10.310][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-07-13 16:04:10.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-07-13 16:04:10.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:10.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:10.315][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-07-13 16:04:10.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-07-13 16:04:10.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:10.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:10.320][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-07-13 16:04:10.321][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-07-13 16:04:10.322][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:10.324][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:10.325][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-07-13 16:04:10.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-07-13 16:04:10.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:10.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:10.345][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:04:10.346][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:04:10.348][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:10.349][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:10.356][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-07-13 16:04:10.357][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-07-13 16:04:10.358][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:10.359][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:10.366][ef$get] Asked field names are: cofactor.
biodb.TRACE[2024-07-13 16:04:10.368][ef$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-07-13 16:04:10.369][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:10.370][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:10.377][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:04:10.378][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:04:10.380][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:10.381][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:10.400][loadFileContents] Loaded 1 files from cache: [1]: "E:/biocbuild/bbs-3.19-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/testref/entry-expasy.enzyme-1.1.1.54-content.txt".
biodb.DEBUG[2024-07-13 16:04:10.430][biodb$getFactory()$createEntryFromCo ...] Creating Expasy ENZYME database. entries from 1 content(s).
biodb.DEBUG[2024-07-13 16:04:10.432][biodb$getFactory()$createEntryFromCo ...] Parsing 1 Expasy ENZYME database. entries.
biodb.DEBUG[2024-07-13 16:04:10.434][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-13 16:04:10.436][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:04:10.438][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:04:10.445][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:10.446][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 16:04:10.447][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:10.448][FUN] Functions in observer BiodbConfig: [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 16:04:10.450][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:04:10.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:04:10.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:10.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:10.456][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-07-13 16:04:10.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-07-13 16:04:10.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:10.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:10.461][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:04:10.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:04:10.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:10.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:10.466][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-07-13 16:04:10.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-07-13 16:04:10.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:10.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:10.471][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-07-13 16:04:10.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-07-13 16:04:10.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:10.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:10.476][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-07-13 16:04:10.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-07-13 16:04:10.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:10.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:10.481][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:04:10.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:04:10.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:10.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:10.490][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-07-13 16:04:10.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-07-13 16:04:10.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:10.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:10.496][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:04:10.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:04:10.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:10.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:10.501][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:04:10.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:04:10.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:10.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:10.505][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:04:10.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:04:10.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:10.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:10.510][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:04:10.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:04:10.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:10.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:10.515][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:04:10.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:04:10.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:10.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:10.520][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:04:10.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:04:10.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:10.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-13 16:04:10.525][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 1.1.1.54.
biodb.TRACE[2024-07-13 16:04:10.544][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-13 16:04:10.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-13 16:04:10.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:10.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:10.549][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-13 16:04:10.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-13 16:04:10.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:10.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:10.554][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-07-13 16:04:10.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-07-13 16:04:10.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:10.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:10.559][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-07-13 16:04:10.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-07-13 16:04:10.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:10.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:10.565][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:04:10.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:04:10.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:10.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:10.575][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-07-13 16:04:10.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-07-13 16:04:10.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:10.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:10.586][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:04:10.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:04:10.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:10.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:10.592][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:04:10.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:04:10.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:10.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:10.596][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:04:10.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:04:10.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:10.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:10.603][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:04:10.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:04:10.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:10.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:10.608][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:04:10.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:04:10.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:10.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:10.613][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:04:10.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:04:10.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:10.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:10.618][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-07-13 16:04:10.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-07-13 16:04:10.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:10.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:10.623][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-07-13 16:04:10.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-07-13 16:04:10.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:10.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:10.628][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-07-13 16:04:10.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-07-13 16:04:10.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:10.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:10.656][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:04:10.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:04:10.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:10.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:10.662][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:04:10.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:04:10.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:10.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:10.666][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:04:10.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:04:10.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:10.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:10.671][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:04:10.673][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:04:10.674][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:10.675][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:10.676][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:04:10.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:04:10.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:10.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:10.691][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:04:10.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:04:10.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:10.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:10.696][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:04:10.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:04:10.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:10.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:10.701][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:04:10.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:04:10.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:10.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:10.705][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:04:10.707][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:04:10.708][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:10.709][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:10.710][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:04:10.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:04:10.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:10.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:10.725][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-07-13 16:04:10.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-07-13 16:04:10.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:10.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:10.730][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-07-13 16:04:10.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-07-13 16:04:10.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:10.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:10.735][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-07-13 16:04:10.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-07-13 16:04:10.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:10.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:10.740][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-07-13 16:04:10.741][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-07-13 16:04:10.742][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:10.743][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:10.744][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-07-13 16:04:10.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-07-13 16:04:10.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:10.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:10.759][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:04:10.760][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:04:10.761][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:10.763][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:10.769][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-07-13 16:04:10.770][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-07-13 16:04:10.772][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:10.773][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:10.779][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:04:10.781][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:04:10.782][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:10.783][ef$get] fields variable is a list.
biodb.INFO [2024-07-13 16:04:10.795][biodb::testThat]
biodb.INFO [2024-07-13 16:04:10.796][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-07-13 16:04:10.797][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-13 16:04:10.798][biodb::testThat]
biodb.DEBUG[2024-07-13 16:04:10.801][private$loadEntries] Creating entries from ids [2]: "1.1.1.1, 1.1.1.54".
biodb.DEBUG[2024-07-13 16:04:10.807][conn$getEntryContent] Get Expasy ENZYME database. entry content(s) for 2 id(s)...
biodb.TRACE[2024-07-13 16:04:10.827][cch$loadFileContent] Trying to load 2 files from cache: [2]: "1.1.1.1, 1.1.1.54".
biodb.INFO [2024-07-13 16:04:10.830][self$getFolderPath] Create cache folder "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280" for "expasy.enzyme-b59b84d962b6741050ba8f70ff4db280".
biodb.TRACE[2024-07-13 16:04:10.832][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2024-07-13 16:04:10.833][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-13 16:04:10.834][conn$getEntryContent] 0 Expasy ENZYME database. entry content(s) loaded from cache.
biodb.DEBUG[2024-07-13 16:04:10.836][conn$getEntryContent] 2 entry content(s) need to be fetched from Expasy ENZYME database. database "https://enzyme.expasy.org/".
biodb.DEBUG[2024-07-13 16:04:10.837][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-13 16:04:10.838][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-13 16:04:10.843][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-13 16:04:10.844][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:04:10.845][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:04:10.858][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:10.860][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:04:10.861][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:10.862][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:04:10.863][scheduler$sendRequest] Getting content of get URL request "https://enzyme.expasy.org/EC/1.1.1.1.txt".
biodb.DEBUG[2024-07-13 16:04:10.881][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-13 16:04:10.883][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-13 16:04:10.884][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/EC/1.1.1.1.txt".
biodb.TRACE[2024-07-13 16:04:11.479][doesRCurlRequestUrlExist] According to RCurl, URL https://enzyme.expasy.org/EC/1.1.1.1.txt does not exist.
biodb.TRACE[2024-07-13 16:04:11.480][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-13 16:04:11.482][getUrlRequestResult] URL "https://enzyme.expasy.org/EC/1.1.1.1.txt" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-13 16:04:11.483][getBaseUrlRequestResult] Using base::url() for sending request (https://enzyme.expasy.org/EC/1.1.1.1.txt).
biodb.DEBUG[2024-07-13 16:04:11.909][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-13 16:04:11.913][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a52675cfd2f0c2b41556caa64d9341e3.content"
biodb.TRACE[2024-07-13 16:04:11.928][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a52675cfd2f0c2b41556caa64d9341e3.request"
biodb.DEBUG[2024-07-13 16:04:11.932][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-13 16:04:11.933][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:04:11.934][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:04:11.942][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:11.945][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 16:04:11.946][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:11.947][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:04:11.966][scheduler$sendRequest] Getting content of get URL request "https://enzyme.expasy.org/EC/1.1.1.54.txt".
biodb.DEBUG[2024-07-13 16:04:11.981][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-13 16:04:11.982][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-13 16:04:12.006][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/EC/1.1.1.54.txt".
biodb.TRACE[2024-07-13 16:04:12.228][doesRCurlRequestUrlExist] According to RCurl, URL https://enzyme.expasy.org/EC/1.1.1.54.txt does not exist.
biodb.TRACE[2024-07-13 16:04:12.229][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-13 16:04:12.230][getUrlRequestResult] URL "https://enzyme.expasy.org/EC/1.1.1.54.txt" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-13 16:04:12.232][getBaseUrlRequestResult] Using base::url() for sending request (https://enzyme.expasy.org/EC/1.1.1.54.txt).
biodb.DEBUG[2024-07-13 16:04:12.658][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-13 16:04:12.660][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a9b93566a091cbe35a06e4b3871f95c9.content"
biodb.TRACE[2024-07-13 16:04:12.665][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a9b93566a091cbe35a06e4b3871f95c9.request"
biodb.TRACE[2024-07-13 16:04:12.668][private$doSaveContentToFile] Saving to cache [2]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/1.1.1.1.txt, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/1.1.1.54.txt"
biodb.DEBUG[2024-07-13 16:04:12.671][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-13 16:04:12.673][self$createEntryFromContent] Creating Expasy ENZYME database. entries from 2 content(s).
biodb.DEBUG[2024-07-13 16:04:12.674][self$createEntryFromContent] Parsing 2 Expasy ENZYME database. entries.
biodb.DEBUG[2024-07-13 16:04:12.676][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-13 16:04:12.677][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:04:12.678][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:04:12.685][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:12.687][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:04:12.688][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:12.689][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-13 16:04:12.692][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:04:12.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:04:12.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:12.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:12.697][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-07-13 16:04:12.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-07-13 16:04:12.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:12.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:12.702][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:04:12.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:04:12.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:12.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:12.707][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-07-13 16:04:12.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-07-13 16:04:12.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:12.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:12.712][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:04:12.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:04:12.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:12.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:12.717][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:04:12.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:04:12.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:12.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:12.722][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:04:12.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:04:12.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:12.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:12.727][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:04:12.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:04:12.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:12.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:12.732][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:04:12.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:04:12.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:12.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:12.737][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-07-13 16:04:12.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-07-13 16:04:12.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:12.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:12.742][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-07-13 16:04:12.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-07-13 16:04:12.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:12.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:12.747][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:04:12.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:04:12.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:12.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:12.752][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-07-13 16:04:12.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-07-13 16:04:12.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:12.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:12.757][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:04:12.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:04:12.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:12.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:12.762][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:04:12.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:04:12.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:12.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:12.767][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:04:12.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:04:12.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:12.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-13 16:04:12.772][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-13 16:04:12.774][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:04:12.775][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:04:12.787][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:12.788][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:04:12.789][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:12.791][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-13 16:04:12.793][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:04:12.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:04:12.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:12.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:12.798][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-07-13 16:04:12.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-07-13 16:04:12.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:12.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:12.803][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:04:12.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:04:12.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:12.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:12.808][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-07-13 16:04:12.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-07-13 16:04:12.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:12.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:12.813][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-07-13 16:04:12.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-07-13 16:04:12.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:12.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:12.818][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-07-13 16:04:12.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-07-13 16:04:12.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:12.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:12.823][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:04:12.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:04:12.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:12.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:12.828][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-07-13 16:04:12.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-07-13 16:04:12.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:12.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:12.833][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:04:12.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:04:12.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:12.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:12.838][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:04:12.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:04:12.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:12.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:12.843][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:04:12.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:04:12.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:12.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:12.848][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:04:12.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:04:12.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:12.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:12.853][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:04:12.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:04:12.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:12.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:12.858][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:04:12.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:04:12.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:12.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:12.863][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:04:12.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:04:12.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:12.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:12.868][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:04:12.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:04:12.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:12.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:12.873][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-13 16:04:12.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-13 16:04:12.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:12.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-13 16:04:12.877][self$createEntryFromContent] Accession numbers: 1.1.1.1, 1.1.1.54.
biodb.TRACE[2024-07-13 16:04:12.879][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-07-13 16:04:12.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-07-13 16:04:12.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:12.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:12.884][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-07-13 16:04:12.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-07-13 16:04:12.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:12.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:12.888][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-07-13 16:04:12.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-07-13 16:04:12.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:12.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:12.899][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-07-13 16:04:12.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-07-13 16:04:12.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:12.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:12.904][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-07-13 16:04:12.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-07-13 16:04:12.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:12.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:12.909][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-07-13 16:04:12.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-07-13 16:04:12.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:12.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-07-13 16:04:12.930][biodb::testThat]
biodb.INFO [2024-07-13 16:04:12.931][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-07-13 16:04:12.933][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-13 16:04:12.934][biodb::testThat]
biodb.TRACE[2024-07-13 16:04:12.937][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:04:12.939][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:04:12.940][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:12.941][ef$get] fields variable is a list.
biodb.DEBUG[2024-07-13 16:04:12.943][function(conn, opt)] Testing searchForEntries() with entry "1.1.1.1" and field "name".
biodb.TRACE[2024-07-13 16:04:12.973][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:04:12.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:04:12.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:12.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:12.978][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:04:12.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:04:12.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:12.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:12.983][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:04:12.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:04:12.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:12.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-13 16:04:12.991][function(conn, opt)] With value "alcohol dehydrogenase".
biodb.DEBUG[2024-07-13 16:04:12.993][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://enzyme.expasy.org/enzyme-byname.html?alcohol dehydrogenase".
biodb.DEBUG[2024-07-13 16:04:12.996][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-13 16:04:12.997][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-13 16:04:12.999][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase".
biodb.TRACE[2024-07-13 16:04:13.220][doesRCurlRequestUrlExist] According to RCurl, URL https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase does not exist.
biodb.TRACE[2024-07-13 16:04:13.222][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-13 16:04:13.223][getUrlRequestResult] URL "https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-13 16:04:13.224][getBaseUrlRequestResult] Using base::url() for sending request (https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase).
biodb.DEBUG[2024-07-13 16:04:13.669][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-13 16:04:13.672][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.content"
biodb.TRACE[2024-07-13 16:04:13.677][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.request"
biodb.DEBUG[2024-07-13 16:04:13.683][function(conn, opt)] With found IDs [1]: "1.1.1.1".
biodb.INFO [2024-07-13 16:04:13.707][biodb::testThat]
biodb.INFO [2024-07-13 16:04:13.708][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-07-13 16:04:13.709][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-13 16:04:13.711][biodb::testThat]
biodb.TRACE[2024-07-13 16:04:13.743][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:04:13.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:04:13.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:13.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:13.748][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:04:13.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:04:13.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:13.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:13.753][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:04:13.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:04:13.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:13.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-13 16:04:13.783][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://enzyme.expasy.org/enzyme-byname.html?alcohol dehydrogenase".
biodb.DEBUG[2024-07-13 16:04:13.787][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-13 16:04:13.800][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f603fa2a57aec59588edc37541c6f6d5".
biodb.TRACE[2024-07-13 16:04:13.802][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-13 16:04:13.806][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.content".
biodb.INFO [2024-07-13 16:04:13.831][biodb::testThat]
biodb.INFO [2024-07-13 16:04:13.833][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-07-13 16:04:13.834][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-13 16:04:13.835][biodb::testThat]
biodb.TRACE[2024-07-13 16:04:13.854][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-13 16:04:13.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-13 16:04:13.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:13.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:13.859][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-13 16:04:13.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-13 16:04:13.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:13.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:13.864][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-07-13 16:04:13.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-07-13 16:04:13.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:13.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:13.868][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-07-13 16:04:13.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-07-13 16:04:13.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:13.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:13.902][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-13 16:04:13.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-13 16:04:13.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:13.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:13.907][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-13 16:04:13.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-13 16:04:13.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:13.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:13.912][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-07-13 16:04:13.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-07-13 16:04:13.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:13.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:13.916][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-07-13 16:04:13.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-07-13 16:04:13.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:13.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-07-13 16:04:13.929][biodb::testThat]
biodb.INFO [2024-07-13 16:04:13.930][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-07-13 16:04:13.932][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-13 16:04:13.933][biodb::testThat]
biodb.INFO [2024-07-13 16:04:13.945][biodb::testThat]
biodb.INFO [2024-07-13 16:04:13.946][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-07-13 16:04:13.948][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-13 16:04:13.949][biodb::testThat]
biodb.INFO [2024-07-13 16:04:13.965][biodb::testThat]
biodb.INFO [2024-07-13 16:04:13.966][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-07-13 16:04:13.967][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-13 16:04:13.968][biodb::testThat]
biodb.DEBUG[2024-07-13 16:04:13.982][function(conn, opt)] Trying to download "https://enzyme.expasy.org/cgi-bin/enzyme/enzyme-search-ec?field1=1&field2=1&field3=1&field4=1".
biodb.DEBUG[2024-07-13 16:04:14.200][getUrlContent] Use base::url() for downloading content of URL https://enzyme.expasy.org/cgi-bin/enzyme/enzyme-search-ec?field1=1&field2=1&field3=1&field4=1.
biodb.INFO [2024-07-13 16:04:14.655][biodb::testThat]
biodb.INFO [2024-07-13 16:04:14.656][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-07-13 16:04:14.657][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-13 16:04:14.658][biodb::testThat]
biodb.DEBUG[2024-07-13 16:04:14.881][getUrlContent] Use base::url() for downloading content of URL https://enzyme.expasy.org/images/1.1.1.1/image.png.
biodb.TRACE[2024-07-13 16:04:15.332][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:04:15.333][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:04:15.335][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:15.336][ef$get] fields variable is a list.
biodb.TRACE[2024-07-13 16:04:15.337][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-13 16:04:15.338][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-13 16:04:15.339][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-13 16:04:15.341][ef$get] fields variable is a list.
biodb.INFO [2024-07-13 16:04:15.342][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-07-13 16:04:15.343][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector expasy.enzyme from the request scheduler
biodb.INFO [2024-07-13 16:04:15.345][self$deleteConn] Connector "expasy.enzyme" deleted.
biodb.DEBUG[2024-07-13 16:04:15.346][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-07-13 16:04:15.347][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:04:15.348][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:04:15.349][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:15.350][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:04:15.351][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:15.352][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-07-13 16:04:15.362][biodb::testContext]
biodb.INFO [2024-07-13 16:04:15.363][biodb::testContext] ********************************************************************************
biodb.INFO [2024-07-13 16:04:15.365][biodb::testContext] Test context - Example long tests
biodb.INFO [2024-07-13 16:04:15.366][biodb::testContext] ********************************************************************************
biodb.INFO [2024-07-13 16:04:15.367][biodb::testContext]
biodb.INFO [2024-07-13 16:04:15.370][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-07-13 16:04:15.372][self$loadDefinitions] Load definitions from file "E:/biocbuild/bbs-3.19-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2024-07-13 16:04:15.378][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-13 16:04:15.379][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-07-13 16:04:15.380][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-07-13 16:04:15.381][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:15.382][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:15.390][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:04:15.391][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-07-13 16:04:15.393][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-07-13 16:04:15.394][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:15.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:15.396][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:04:15.397][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-07-13 16:04:15.398][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-07-13 16:04:15.399][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:15.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:15.402][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:04:15.403][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-07-13 16:04:15.404][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-07-13 16:04:15.405][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-07-13 16:04:15.406][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:15.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:15.409][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:04:15.410][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-07-13 16:04:15.411][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-07-13 16:04:15.412][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-07-13 16:04:15.413][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:15.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:15.415][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:04:15.417][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-07-13 16:04:15.418][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-07-13 16:04:15.419][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:15.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:15.421][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:04:15.422][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-07-13 16:04:15.424][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-07-13 16:04:15.425][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-07-13 16:04:15.426][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:15.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:15.428][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:04:15.429][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-07-13 16:04:15.431][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-07-13 16:04:15.432][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:15.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:15.434][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:04:15.435][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-07-13 16:04:15.436][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-07-13 16:04:15.438][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-07-13 16:04:15.440][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:15.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:15.442][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:04:15.443][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-07-13 16:04:15.445][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-07-13 16:04:15.446][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-07-13 16:04:15.447][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-07-13 16:04:15.448][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-07-13 16:04:15.449][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-07-13 16:04:15.451][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:15.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:15.453][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:04:15.454][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-07-13 16:04:15.455][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-07-13 16:04:15.456][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:15.457][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:15.459][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 16:04:15.460][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-07-13 16:04:15.461][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-07-13 16:04:15.462][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:15.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:15.464][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:04:15.465][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-07-13 16:04:15.467][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-07-13 16:04:15.468][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:15.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:15.470][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:04:15.471][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-07-13 16:04:15.472][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-07-13 16:04:15.474][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:15.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:15.476][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:04:15.477][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-07-13 16:04:15.478][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-07-13 16:04:15.479][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:15.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:15.481][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:04:15.483][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-07-13 16:04:15.484][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-07-13 16:04:15.487][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-07-13 16:04:15.488][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:15.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:15.491][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:04:15.492][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-07-13 16:04:15.493][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-07-13 16:04:15.494][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-07-13 16:04:15.495][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:15.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:15.498][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:04:15.499][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-07-13 16:04:15.501][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-13 16:04:15.502][self$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 16:04:15.503][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-13 16:04:15.505][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-13 16:04:15.506][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-13 16:04:15.507][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-13 16:04:15.508][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-13 16:04:15.510][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-13 16:04:15.511][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-13 16:04:15.518][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-13 16:04:15.519][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-13 16:04:15.520][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-07-13 16:04:15.521][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-13 16:04:15.523][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:04:15.524][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-13 16:04:15.525][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-13 16:04:15.525][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-13 16:04:15.525][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-13 16:04:15.525][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-07-13 16:04:15.525][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-07-13 16:04:15.526][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-13 16:04:15.527][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-13 16:04:15.528][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-13 16:04:15.530][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-13 16:04:15.531][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-13 16:04:15.532][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-13 16:04:15.533][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-13 16:04:15.534][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:04:15.535][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-13 16:04:15.537][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-13 16:04:15.538][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-13 16:04:15.539][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:04:15.540][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-07-13 16:04:15.542][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-13 16:04:15.543][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-07-13 16:04:15.545][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-13 16:04:15.546][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-13 16:04:15.547][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-13 16:04:15.548][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-13 16:04:15.549][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-13 16:04:15.551][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-13 16:04:15.552][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-07-13 16:04:15.553][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-13 16:04:15.554][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-13 16:04:15.556][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-07-13 16:04:15.557][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-13 16:04:15.558][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:04:15.559][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-13 16:04:15.560][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-13 16:04:15.560][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-13 16:04:15.560][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-13 16:04:15.560][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-07-13 16:04:15.560][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-07-13 16:04:15.562][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-13 16:04:15.563][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-13 16:04:15.564][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-13 16:04:15.565][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-13 16:04:15.566][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-13 16:04:15.567][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-13 16:04:15.569][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-13 16:04:15.570][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:04:15.571][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-13 16:04:15.572][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-13 16:04:15.573][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-13 16:04:15.575][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:04:15.576][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-07-13 16:04:15.578][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-07-13 16:04:15.579][self$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 16:04:15.580][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-13 16:04:15.582][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-13 16:04:15.583][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-13 16:04:15.584][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-13 16:04:15.585][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-13 16:04:15.586][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-13 16:04:15.588][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-13 16:04:15.589][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-13 16:04:15.590][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-07-13 16:04:15.591][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-07-13 16:04:15.592][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-13 16:04:15.594][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:04:15.595][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-13 16:04:15.596][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:04:15.597][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-13 16:04:15.598][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-13 16:04:15.600][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-13 16:04:15.601][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-13 16:04:15.602][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-13 16:04:15.603][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-13 16:04:15.604][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-13 16:04:15.605][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:04:15.606][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-13 16:04:15.607][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-13 16:04:15.609][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-13 16:04:15.610][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:04:15.611][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-07-13 16:04:15.613][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-07-13 16:04:15.614][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-07-13 16:04:15.616][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-13 16:04:15.617][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-13 16:04:15.618][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-13 16:04:15.619][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-13 16:04:15.620][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-13 16:04:15.622][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-13 16:04:15.623][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-07-13 16:04:15.624][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-13 16:04:15.625][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-07-13 16:04:15.626][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-07-13 16:04:15.628][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-13 16:04:15.629][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:04:15.630][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-13 16:04:15.631][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:04:15.632][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-13 16:04:15.638][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-13 16:04:15.640][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-13 16:04:15.641][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-13 16:04:15.642][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-13 16:04:15.643][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-13 16:04:15.644][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-13 16:04:15.646][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:04:15.647][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-13 16:04:15.648][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-13 16:04:15.649][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-13 16:04:15.650][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:04:15.652][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-13 16:04:15.653][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:15.654][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:04:15.655][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:15.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:15.657][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 16:04:15.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:15.659][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:04:15.660][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:15.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:15.663][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 16:04:15.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:15.665][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:04:15.666][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:15.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:15.668][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 16:04:15.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:15.670][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:04:15.671][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:15.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:15.674][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 16:04:15.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:15.676][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:04:15.677][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:15.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:15.679][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 16:04:15.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:15.681][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:04:15.682][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:15.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:15.685][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:04:15.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:15.687][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:04:15.688][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:15.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:15.690][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 16:04:15.691][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:15.692][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:04:15.693][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:15.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:15.696][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 16:04:15.697][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:15.698][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:04:15.699][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:15.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:15.701][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 16:04:15.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:15.703][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:04:15.704][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:15.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:15.706][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 16:04:15.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:15.709][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:04:15.710][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:15.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:15.712][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 16:04:15.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:15.714][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:04:15.715][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:15.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:15.717][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 16:04:15.718][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:15.719][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:04:15.721][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:15.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:15.723][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:04:15.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:15.725][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:04:15.726][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:15.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:15.728][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 16:04:15.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:15.730][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:04:15.731][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:15.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:15.734][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 16:04:15.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:15.736][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:04:15.737][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:15.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:15.739][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:04:15.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:15.741][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:04:15.742][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:15.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:15.744][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 16:04:15.745][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:15.747][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-13 16:04:15.748][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-07-13 16:04:15.749][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-07-13 16:04:15.751][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-07-13 16:04:15.753][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-07-13 16:04:15.754][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-07-13 16:04:15.761][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-07-13 16:04:15.762][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-07-13 16:04:15.764][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-07-13 16:04:15.765][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-07-13 16:04:15.767][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-07-13 16:04:15.768][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-07-13 16:04:15.770][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-07-13 16:04:15.772][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-07-13 16:04:15.773][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-07-13 16:04:15.775][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-07-13 16:04:15.776][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-07-13 16:04:15.778][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-07-13 16:04:15.779][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-07-13 16:04:15.781][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-07-13 16:04:15.782][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-07-13 16:04:15.784][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-07-13 16:04:15.786][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-07-13 16:04:15.787][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-07-13 16:04:15.789][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-07-13 16:04:15.790][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-07-13 16:04:15.792][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-07-13 16:04:15.794][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-07-13 16:04:15.795][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-07-13 16:04:15.797][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-07-13 16:04:15.798][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-07-13 16:04:15.800][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-07-13 16:04:15.801][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-07-13 16:04:15.803][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-07-13 16:04:15.805][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-07-13 16:04:15.806][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-07-13 16:04:15.808][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-07-13 16:04:15.809][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-07-13 16:04:15.811][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-07-13 16:04:15.812][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-07-13 16:04:15.814][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-07-13 16:04:15.816][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-07-13 16:04:15.817][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-07-13 16:04:15.819][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-07-13 16:04:15.820][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-07-13 16:04:15.822][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-07-13 16:04:15.823][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-07-13 16:04:15.825][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-07-13 16:04:15.826][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-07-13 16:04:15.828][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-07-13 16:04:15.830][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-07-13 16:04:15.831][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-07-13 16:04:15.833][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-07-13 16:04:15.834][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-07-13 16:04:15.836][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-07-13 16:04:15.838][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-07-13 16:04:15.839][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-07-13 16:04:15.841][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-07-13 16:04:15.842][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-07-13 16:04:15.844][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-07-13 16:04:15.845][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-07-13 16:04:15.847][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-07-13 16:04:15.848][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-07-13 16:04:15.850][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-07-13 16:04:15.851][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-07-13 16:04:15.853][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-07-13 16:04:15.855][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-07-13 16:04:15.856][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-07-13 16:04:15.858][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-07-13 16:04:15.859][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-07-13 16:04:15.861][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-07-13 16:04:15.862][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-07-13 16:04:15.864][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-07-13 16:04:15.871][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-07-13 16:04:15.873][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-07-13 16:04:15.874][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-07-13 16:04:15.876][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-07-13 16:04:15.877][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-07-13 16:04:15.879][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-07-13 16:04:15.880][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-07-13 16:04:15.882][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-07-13 16:04:15.884][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-07-13 16:04:15.885][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-07-13 16:04:15.887][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-07-13 16:04:15.888][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-07-13 16:04:15.891][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-07-13 16:04:15.892][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-13 16:04:15.893][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:15.894][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 16:04:15.895][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:15.896][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 16:04:15.897][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:15.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:04:15.900][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:04:15.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:15.902][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 16:04:15.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:15.904][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:04:15.905][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:15.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:04:15.907][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:04:15.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:15.909][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 16:04:15.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:15.912][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:04:15.913][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:15.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:04:15.915][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:04:15.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:15.917][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 16:04:15.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:15.920][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:04:15.921][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:15.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:04:15.923][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:04:15.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:15.925][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 16:04:15.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:15.927][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:04:15.928][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:15.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:04:15.931][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:04:15.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:15.933][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 16:04:15.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:15.935][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:04:15.936][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:15.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:04:15.938][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:04:15.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:15.940][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 16:04:15.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:15.943][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:04:15.944][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:15.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:04:15.946][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:04:15.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:15.948][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 16:04:15.949][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:15.950][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:04:15.951][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:15.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:04:15.953][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:04:15.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:15.956][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 16:04:15.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:15.958][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:04:15.959][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:15.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:04:15.961][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:04:15.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:15.963][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-13 16:04:15.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:15.966][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:04:15.967][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:15.968][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:04:15.969][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:04:15.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:15.971][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 16:04:15.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:15.973][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:04:15.975][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:15.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:04:15.977][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:04:15.978][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:15.979][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 16:04:15.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:15.981][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:04:15.982][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:15.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:04:15.990][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:04:15.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:15.992][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 16:04:15.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:15.994][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:04:15.995][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:15.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:04:15.997][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:04:15.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:16.000][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 16:04:16.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:16.002][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:04:16.003][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:16.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:04:16.005][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:04:16.006][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:16.007][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 16:04:16.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:16.010][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:04:16.011][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:16.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:04:16.013][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:04:16.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:16.015][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 16:04:16.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:16.017][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:04:16.018][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:16.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:04:16.021][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:04:16.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:16.023][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 16:04:16.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:16.025][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:04:16.026][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-13 16:04:16.027][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:04:16.028][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:04:16.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:16.031][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 16:04:16.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:16.033][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:04:16.036][biodb$loadDefinitions] Load definitions from file "E:/biocbuild/bbs-3.19-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/definitions.yml".
biodb.DEBUG[2024-07-13 16:04:16.038][self$getDbsInfo()$define] Define connector expasy.enzyme.
biodb.DEBUG[2024-07-13 16:04:16.040][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-13 16:04:16.041][self$setPropertyValue] Setting property "description" to "Write here the description of this database.".
biodb.DEBUG[2024-07-13 16:04:16.043][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-13 16:04:16.044][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-13 16:04:16.045][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-13 16:04:16.046][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-13 16:04:16.047][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-07-13 16:04:16.049][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-13 16:04:16.050][self$setPropertyValue] Setting property "entry.content.type" to "txt".
biodb.DEBUG[2024-07-13 16:04:16.051][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-13 16:04:16.052][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-13 16:04:16.054][self$setPropertyValue] Setting property "name" to "Expasy ENZYME database.".
biodb.DEBUG[2024-07-13 16:04:16.055][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-13 16:04:16.056][self$setPropertyValue] Setting property "parsing.expr" to "^ID\s+([0-9.]+)$".
biodb.DEBUG[2024-07-13 16:04:16.056][self$setPropertyValue] Setting property "parsing.expr" to "^CA\s+(.+?)\.?$".
biodb.DEBUG[2024-07-13 16:04:16.056][self$setPropertyValue] Setting property "parsing.expr" to "^CF\s+(.+?)\.?$".
biodb.DEBUG[2024-07-13 16:04:16.056][self$setPropertyValue] Setting property "parsing.expr" to "^DE\s+(.+?)\.?$".
biodb.DEBUG[2024-07-13 16:04:16.057][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-07-13 16:04:16.058][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-13 16:04:16.060][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-07-13 16:04:16.061][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-13 16:04:16.062][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-13 16:04:16.063][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-13 16:04:16.064][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-13 16:04:16.065][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-13 16:04:16.067][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-13 16:04:16.068][self$setPropertyValue] Setting property "urls" to "https://enzyme.expasy.org/".
biodb.DEBUG[2024-07-13 16:04:16.069][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-13 16:04:16.070][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-13 16:04:16.071][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-07-13 16:04:16.072][self$setPropertyValue]
biodb.DEBUG[2024-07-13 16:04:16.074][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-07-13 16:04:16.077][super$initialize] Initialize connector expasy.enzyme.
biodb.DEBUG[2024-07-13 16:04:16.079][super$initialize] Register connector expasy.enzyme with the request scheduler
biodb.DEBUG[2024-07-13 16:04:16.080][private$bdb$getRequestScheduler()$re ...] Register connector expasy.enzyme.
biodb.DEBUG[2024-07-13 16:04:16.082][private$addConnectorRules] Create new rule for URL "enzyme.expasy.org" of connector "expasy.enzyme".
biodb.DEBUG[2024-07-13 16:04:16.083][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-07-13 16:04:16.085][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-07-13 16:04:16.086][biodb$getFactory()$createConn] Creating new connector expasy.enzyme for database class expasy.enzyme .
biodb.INFO [2024-07-13 16:04:16.087][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-07-13 16:04:16.088][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector expasy.enzyme from the request scheduler
biodb.INFO [2024-07-13 16:04:16.090][self$deleteConn] Connector "expasy.enzyme" deleted.
biodb.DEBUG[2024-07-13 16:04:16.091][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-07-13 16:04:16.092][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-13 16:04:16.093][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-13 16:04:16.094][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-13 16:04:16.095][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 16:04:16.096][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-07-13 16:04:16.097][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".
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 85 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_long_100_generic.R:37:1'): The entry image URL can be downloaded. ──
Error in `charToRaw(content)`: argument must be a character vector of length 1
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<ExpsyEnC>`, opt = `<named list>`)
 3.   └─biodb:::getUrlContent(url, binary = TRUE)
 4.     └─biodb:::getBaseUrlContent(u, binary = binary)
 5.       └─base::charToRaw(content)

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 85 ]
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 biodbExpasy_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbuild/bbs-3.19-bioc-longtests/meat/biodbExpasy.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 'biodbExpasy/DESCRIPTION' ... OK
* this is package 'biodbExpasy' version '1.8.0'
* 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 'biodbExpasy' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... SKIPPED
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... 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:
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_long_100_generic.R:37:1'): The entry image URL can be downloaded. ──
  Error in `charToRaw(content)`: argument must be a character vector of length 1
  Backtrace:
      ▆
   1. ├─base::do.call(fct, params)
   2. └─biodb (local) `<fn>`(conn = `<ExpsyEnC>`, opt = `<named list>`)
   3.   └─biodb:::getUrlContent(url, binary = TRUE)
   4.     └─biodb:::getBaseUrlContent(u, binary = binary)
   5.       └─base::charToRaw(content)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 85 ]
  Error: Test failures
  Execution halted
* DONE

Status: 1 ERROR, 1 NOTE
See
  'E:/biocbuild/bbs-3.19-bioc-longtests/meat/biodbExpasy.Rcheck/00check.log'
for details.


Installation output

biodbExpasy.Rcheck/00install.out

* installing *source* package 'biodbExpasy' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** 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 (biodbExpasy)