Back to Long Tests report for BioC 3.20

This page was generated on 2024-06-15 23:55 -0400 (Sat, 15 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4685
palomino4Windows Server 2022 Datacenterx644.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 4420
lconwaymacOS 12.7.1 Montereyx86_644.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" 4400
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 7/32HostnameOS / ArchCHECK
biodbExpasy 1.9.0  (landing page)
Pierrick Roger
Snapshot Date: 2024-06-15 09:55 -0400 (Sat, 15 Jun 2024)
git_url: https://git.bioconductor.org/packages/biodbExpasy
git_branch: devel
git_last_commit: 25fc0fc
git_last_commit_date: 2024-04-30 11:41:12 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  ERROR  
palomino4Windows Server 2022 Datacenter / x64  ERROR  
lconwaymacOS 12.7.1 Monterey / x86_64  ERROR  

CHECK results for biodbExpasy on palomino4

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: 1.9.0
Command: F:\biocbuild\bbs-3.20-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_1.9.0.tar.gz
StartedAt: 2024-06-15 16:16:03 -0400 (Sat, 15 Jun 2024)
EndedAt: 2024-06-15 16:22:32 -0400 (Sat, 15 Jun 2024)
EllapsedTime: 389.3 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbExpasy.Rcheck
Warnings: NA

Tests output

biodbExpasy.Rcheck/tests/testthat.Rout.fail


R version 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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Type 'license()' or 'licence()' for distribution details.

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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 [2024-06-15 16:22:21.960][biodb::testContext]
biodb.INFO [2024-06-15 16:22:21.973][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-15 16:22:21.975][biodb::testContext] Test context - Generic long tests
biodb.INFO [2024-06-15 16:22:21.977][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-15 16:22:21.978][biodb::testContext]
biodb.INFO [2024-06-15 16:22:21.986][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.13.0.
biodb.DEBUG[2024-06-15 16:22:21.990][self$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.20-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2024-06-15 16:22:22.000][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-15 16:22:22.002][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-06-15 16:22:22.003][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-06-15 16:22:22.004][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:22.006][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:22.007][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:22:22.009][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-06-15 16:22:22.052][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-06-15 16:22:22.054][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:22.056][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:22.057][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:22:22.059][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-06-15 16:22:22.061][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-06-15 16:22:22.063][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:22.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:22.066][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:22:22.068][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-06-15 16:22:22.070][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-06-15 16:22:22.072][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-06-15 16:22:22.074][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:22.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:22.077][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:22:22.079][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-06-15 16:22:22.081][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-06-15 16:22:22.083][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-06-15 16:22:22.084][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:22.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:22.088][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:22:22.090][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-06-15 16:22:22.092][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-06-15 16:22:22.093][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:22.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:22.097][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:22:22.099][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-06-15 16:22:22.101][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-06-15 16:22:22.103][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-06-15 16:22:22.104][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:22.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:22.108][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:22:22.110][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-06-15 16:22:22.112][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-06-15 16:22:22.113][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:22.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:22.117][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:22:22.118][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-06-15 16:22:22.120][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-06-15 16:22:22.122][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-06-15 16:22:22.124][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:22.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:22.127][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:22:22.129][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-06-15 16:22:22.131][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-06-15 16:22:22.133][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-06-15 16:22:22.135][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-06-15 16:22:22.137][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-06-15 16:22:22.139][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-06-15 16:22:22.141][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:22.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:22.144][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:22:22.146][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-06-15 16:22:22.148][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-06-15 16:22:22.149][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:22.151][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:22.152][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:22:22.154][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-06-15 16:22:22.156][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-06-15 16:22:22.158][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:22.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:22.161][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:22:22.163][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-06-15 16:22:22.165][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-06-15 16:22:22.167][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:22.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:22.171][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:22:22.173][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-06-15 16:22:22.175][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-06-15 16:22:22.177][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:22.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:22.180][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:22:22.182][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-06-15 16:22:22.184][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-06-15 16:22:22.186][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:22.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:22.190][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:22:22.191][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-06-15 16:22:22.193][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-06-15 16:22:22.199][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-06-15 16:22:22.201][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:22.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:22.205][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:22:22.207][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-06-15 16:22:22.209][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-06-15 16:22:22.211][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-06-15 16:22:22.212][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:22.214][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:22.216][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:22:22.221][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-06-15 16:22:22.270][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-15 16:22:22.294][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-06-15 16:22:22.297][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-15 16:22:22.299][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-15 16:22:22.301][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-15 16:22:22.303][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-15 16:22:22.305][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-15 16:22:22.307][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-15 16:22:22.309][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-15 16:22:22.311][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-15 16:22:22.313][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-15 16:22:22.315][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-06-15 16:22:22.317][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-15 16:22:22.319][self$setPropertyValue]
biodb.DEBUG[2024-06-15 16:22:22.321][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-15 16:22:22.323][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-15 16:22:22.323][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-15 16:22:22.323][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-15 16:22:22.323][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-15 16:22:22.323][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-15 16:22:22.325][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-15 16:22:22.327][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-15 16:22:22.329][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-15 16:22:22.331][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-15 16:22:22.333][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-15 16:22:22.335][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-15 16:22:22.337][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-15 16:22:22.347][self$setPropertyValue]
biodb.DEBUG[2024-06-15 16:22:22.350][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-15 16:22:22.351][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-15 16:22:22.353][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-15 16:22:22.355][self$setPropertyValue]
biodb.DEBUG[2024-06-15 16:22:22.358][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-06-15 16:22:22.361][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-15 16:22:22.363][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-06-15 16:22:22.365][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-15 16:22:22.367][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-15 16:22:22.368][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-15 16:22:22.370][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-15 16:22:22.372][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-15 16:22:22.374][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-15 16:22:22.376][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-15 16:22:22.378][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-15 16:22:22.380][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-15 16:22:22.382][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-06-15 16:22:22.384][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-15 16:22:22.386][self$setPropertyValue]
biodb.DEBUG[2024-06-15 16:22:22.387][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-15 16:22:22.389][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-15 16:22:22.389][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-15 16:22:22.389][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-15 16:22:22.389][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-15 16:22:22.389][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-15 16:22:22.391][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-15 16:22:22.393][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-15 16:22:22.395][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-15 16:22:22.397][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-15 16:22:22.399][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-15 16:22:22.401][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-15 16:22:22.403][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-15 16:22:22.404][self$setPropertyValue]
biodb.DEBUG[2024-06-15 16:22:22.406][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-15 16:22:22.408][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-15 16:22:22.410][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-15 16:22:22.412][self$setPropertyValue]
biodb.DEBUG[2024-06-15 16:22:22.414][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-06-15 16:22:22.417][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-15 16:22:22.419][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-06-15 16:22:22.421][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-15 16:22:22.423][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-15 16:22:22.425][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-15 16:22:22.427][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-15 16:22:22.429][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-15 16:22:22.431][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-15 16:22:22.433][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-15 16:22:22.435][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-15 16:22:22.437][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-15 16:22:22.439][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-06-15 16:22:22.441][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-15 16:22:22.443][self$setPropertyValue]
biodb.DEBUG[2024-06-15 16:22:22.445][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-15 16:22:22.447][self$setPropertyValue]
biodb.DEBUG[2024-06-15 16:22:22.449][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-15 16:22:22.450][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-15 16:22:22.452][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-15 16:22:22.454][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-15 16:22:22.456][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-15 16:22:22.458][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-15 16:22:22.460][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-15 16:22:22.462][self$setPropertyValue]
biodb.DEBUG[2024-06-15 16:22:22.464][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-15 16:22:22.465][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-15 16:22:22.467][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-15 16:22:22.469][self$setPropertyValue]
biodb.DEBUG[2024-06-15 16:22:22.471][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-06-15 16:22:22.475][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-15 16:22:22.476][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-06-15 16:22:22.478][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-15 16:22:22.480][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-15 16:22:22.482][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-15 16:22:22.484][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-15 16:22:22.486][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-15 16:22:22.488][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-15 16:22:22.490][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-15 16:22:22.492][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-15 16:22:22.494][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-15 16:22:22.496][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-06-15 16:22:22.498][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-15 16:22:22.500][self$setPropertyValue]
biodb.DEBUG[2024-06-15 16:22:22.502][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-15 16:22:22.504][self$setPropertyValue]
biodb.DEBUG[2024-06-15 16:22:22.506][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-15 16:22:22.508][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-15 16:22:22.510][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-15 16:22:22.511][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-15 16:22:22.513][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-15 16:22:22.515][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-15 16:22:22.517][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-15 16:22:22.519][self$setPropertyValue]
biodb.DEBUG[2024-06-15 16:22:22.521][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-15 16:22:22.523][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-15 16:22:22.525][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-15 16:22:22.526][self$setPropertyValue]
biodb.DEBUG[2024-06-15 16:22:22.532][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-15 16:22:22.534][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:22.535][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:22:22.537][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:22.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:22:22.541][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:22:22.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:22.545][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:22:22.546][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:22.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:22:22.550][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:22:22.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:22.554][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:22:22.555][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:22.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:22:22.559][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:22:22.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:22.562][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:22:22.564][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:22.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:22:22.568][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:22:22.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:22.571][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:22:22.573][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:22.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:22:22.577][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:22:22.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:22.580][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[2024-06-15 16:22:22.582][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:22.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:22:22.586][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:22:22.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:22.589][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:22:22.591][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:22.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:22:22.594][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:22:22.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:22.598][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:22:22.600][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:22.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:22:22.603][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:22:22.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:22.607][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:22:22.608][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:22.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:22:22.612][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:22:22.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:22.615][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:22:22.617][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:22.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:22:22.620][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:22:22.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:22.624][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:22:22.626][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:22.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:22:22.629][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:22:22.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:22.633][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:22:22.635][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:22.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:22:22.638][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:22:22.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:22.640][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:22:22.641][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:22.642][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:22:22.643][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:22:22.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:22.646][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:22:22.647][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:22.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:22:22.649][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:22:22.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:22.651][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:22:22.652][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:22.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:22:22.655][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:22:22.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:22.657][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:22:22.658][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:22.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:22:22.660][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:22:22.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:22.662][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:22:22.664][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:22.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:22:22.666][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:22:22.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:22.668][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:22:22.669][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-06-15 16:22:22.679][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-06-15 16:22:22.681][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-06-15 16:22:22.682][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-06-15 16:22:22.684][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-15 16:22:22.685][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-15 16:22:22.687][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-06-15 16:22:22.689][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-06-15 16:22:22.690][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-15 16:22:22.692][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-15 16:22:22.693][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-15 16:22:22.695][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-06-15 16:22:22.696][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-06-15 16:22:22.698][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-06-15 16:22:22.699][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-06-15 16:22:22.701][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-15 16:22:22.703][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-06-15 16:22:22.704][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-06-15 16:22:22.706][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-15 16:22:22.707][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-06-15 16:22:22.709][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-06-15 16:22:22.711][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-06-15 16:22:22.713][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-06-15 16:22:22.714][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-06-15 16:22:22.716][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-06-15 16:22:22.717][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-06-15 16:22:22.719][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-06-15 16:22:22.721][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-06-15 16:22:22.722][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-06-15 16:22:22.724][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-06-15 16:22:22.725][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-06-15 16:22:22.727][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-06-15 16:22:22.728][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-06-15 16:22:22.730][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-06-15 16:22:22.732][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-06-15 16:22:22.733][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-06-15 16:22:22.735][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-06-15 16:22:22.736][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-06-15 16:22:22.738][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-06-15 16:22:22.739][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-06-15 16:22:22.741][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-06-15 16:22:22.743][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-06-15 16:22:22.744][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-06-15 16:22:22.746][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-06-15 16:22:22.747][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-06-15 16:22:22.749][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-06-15 16:22:22.751][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-06-15 16:22:22.752][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-06-15 16:22:22.754][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-06-15 16:22:22.755][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-06-15 16:22:22.757][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-06-15 16:22:22.759][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-06-15 16:22:22.760][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-06-15 16:22:22.762][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-06-15 16:22:22.763][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-06-15 16:22:22.765][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-06-15 16:22:22.766][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-06-15 16:22:22.768][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-06-15 16:22:22.770][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-06-15 16:22:22.771][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-06-15 16:22:22.773][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-06-15 16:22:22.774][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-06-15 16:22:22.776][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-06-15 16:22:22.777][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-06-15 16:22:22.779][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-06-15 16:22:22.781][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-06-15 16:22:22.782][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-15 16:22:22.784][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-15 16:22:22.785][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-06-15 16:22:22.787][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-06-15 16:22:22.788][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-06-15 16:22:22.790][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-06-15 16:22:22.792][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-06-15 16:22:22.793][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-06-15 16:22:22.796][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-06-15 16:22:22.798][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-06-15 16:22:22.800][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-06-15 16:22:22.803][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-06-15 16:22:22.805][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-06-15 16:22:22.807][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-06-15 16:22:22.810][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-06-15 16:22:22.812][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-06-15 16:22:22.814][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-06-15 16:22:22.865][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-06-15 16:22:22.870][initialize] This is biodb version 1.13.0.
biodb.DEBUG[2024-06-15 16:22:22.873][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-15 16:22:22.875][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:22:22.876][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:22:22.877][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:22.879][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:22:22.885][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:22.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-15 16:22:22.888][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-15 16:22:22.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:22:22.892][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:22:22.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:22.895][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:22:22.896][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:22.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-15 16:22:22.898][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-15 16:22:22.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:22:22.901][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:22:22.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:22.903][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:22:22.904][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:22.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-15 16:22:22.907][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-15 16:22:22.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:22:22.909][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:22:22.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:22.911][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:22:22.912][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:22.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-15 16:22:22.915][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-15 16:22:22.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:22:22.917][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:22:22.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:22.919][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:22:22.920][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:22.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-15 16:22:22.922][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-15 16:22:22.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:22:22.925][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:22:22.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:22.927][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[2024-06-15 16:22:22.928][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:22.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-15 16:22:22.930][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-15 16:22:22.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:22:22.939][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:22:22.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:22.941][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[2024-06-15 16:22:22.942][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:22.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-15 16:22:22.944][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-15 16:22:22.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:22:22.946][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:22:22.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:22.949][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:22:22.950][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:22.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-15 16:22:22.952][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-15 16:22:22.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:22:22.954][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:22:22.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:22.956][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:22:22.957][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:22.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-15 16:22:22.959][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-15 16:22:22.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:22:22.962][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:22:22.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:22.964][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:22:22.965][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:22.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-15 16:22:22.967][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-15 16:22:22.968][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:22:22.969][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:22:22.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:22.972][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[2024-06-15 16:22:22.973][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:22.974][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-15 16:22:22.975][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-15 16:22:22.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:22:22.978][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:22:22.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:22.981][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[2024-06-15 16:22:22.982][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:22.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-15 16:22:22.985][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-15 16:22:22.987][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:22:22.988][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:22:22.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:22.992][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:22:22.993][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:22.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-15 16:22:22.996][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-15 16:22:22.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:22:22.999][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:22:23.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:23.003][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:22:23.004][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:23.006][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-15 16:22:23.007][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-15 16:22:23.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:22:23.010][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:22:23.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:23.014][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:22:23.015][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:23.017][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-15 16:22:23.018][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-15 16:22:23.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:22:23.021][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:22:23.023][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:23.025][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[2024-06-15 16:22:23.026][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:23.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-15 16:22:23.029][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-15 16:22:23.031][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:22:23.033][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:22:23.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:23.036][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:22:23.037][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:23.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-15 16:22:23.039][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-15 16:22:23.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:22:23.041][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:22:23.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:23.043][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:22:23.048][biodb$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/definitions.yml".
biodb.DEBUG[2024-06-15 16:22:23.058][self$getDbsInfo()$define] Define connector expasy.enzyme.
biodb.DEBUG[2024-06-15 16:22:23.060][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-15 16:22:23.061][self$setPropertyValue] Setting property "description" to "Write here the description of this database.".
biodb.DEBUG[2024-06-15 16:22:23.063][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-15 16:22:23.064][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-15 16:22:23.065][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-15 16:22:23.067][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-15 16:22:23.068][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-06-15 16:22:23.069][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-15 16:22:23.070][self$setPropertyValue] Setting property "entry.content.type" to "txt".
biodb.DEBUG[2024-06-15 16:22:23.072][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-15 16:22:23.073][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-15 16:22:23.074][self$setPropertyValue] Setting property "name" to "Expasy ENZYME database.".
biodb.DEBUG[2024-06-15 16:22:23.076][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-15 16:22:23.077][self$setPropertyValue] Setting property "parsing.expr" to "^ID\s+([0-9.]+)$".
biodb.DEBUG[2024-06-15 16:22:23.077][self$setPropertyValue] Setting property "parsing.expr" to "^CA\s+(.+?)\.?$".
biodb.DEBUG[2024-06-15 16:22:23.077][self$setPropertyValue] Setting property "parsing.expr" to "^CF\s+(.+?)\.?$".
biodb.DEBUG[2024-06-15 16:22:23.077][self$setPropertyValue] Setting property "parsing.expr" to "^DE\s+(.+?)\.?$".
biodb.DEBUG[2024-06-15 16:22:23.078][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-06-15 16:22:23.079][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-15 16:22:23.081][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-06-15 16:22:23.082][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-15 16:22:23.083][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-15 16:22:23.084][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-15 16:22:23.085][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-15 16:22:23.086][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-15 16:22:23.087][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-15 16:22:23.089][self$setPropertyValue] Setting property "urls" to "https://enzyme.expasy.org/".
biodb.DEBUG[2024-06-15 16:22:23.090][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-15 16:22:23.091][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-15 16:22:23.092][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-06-15 16:22:23.094][self$setPropertyValue]
biodb.DEBUG[2024-06-15 16:22:23.100][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-15 16:22:23.126][super$initialize] Initialize connector expasy.enzyme.
biodb.DEBUG[2024-06-15 16:22:23.129][super$initialize] Register connector expasy.enzyme with the request scheduler
biodb.DEBUG[2024-06-15 16:22:23.135][private$bdb$getRequestScheduler()$re ...] Register connector expasy.enzyme.
biodb.DEBUG[2024-06-15 16:22:23.142][private$addConnectorRules] Create new rule for URL "enzyme.expasy.org" of connector "expasy.enzyme".
biodb.DEBUG[2024-06-15 16:22:23.147][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-15 16:22:23.149][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-15 16:22:23.152][biodb$getFactory()$createConn] Creating new connector expasy.enzyme for database class expasy.enzyme .
biodb.INFO [2024-06-15 16:22:23.167][biodb::testThat]
biodb.INFO [2024-06-15 16:22:23.170][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-06-15 16:22:23.171][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-15 16:22:23.173][biodb::testThat]
biodb.TRACE[2024-06-15 16:22:23.182][loadFileContents] Loaded 1 files from cache: [1]: "F:/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/testref/entry-expasy.enzyme-1.1.1.1-content.txt".
biodb.DEBUG[2024-06-15 16:22:23.185][biodb$getFactory()$createEntryFromCo ...] Creating Expasy ENZYME database. entries from 1 content(s).
biodb.DEBUG[2024-06-15 16:22:23.190][biodb$getFactory()$createEntryFromCo ...] Parsing 1 Expasy ENZYME database. entries.
biodb.DEBUG[2024-06-15 16:22:23.201][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-15 16:22:23.203][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-15 16:22:23.213][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-15 16:22:23.244][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:22:23.246][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:22:23.248][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:23.250][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.TRACE[2024-06-15 16:22:23.264][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-15 16:22:23.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-15 16:22:23.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:23.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:23.308][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-15 16:22:23.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-15 16:22:23.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:23.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:23.333][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-15 16:22:23.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-15 16:22:23.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:23.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:23.341][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-15 16:22:23.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-15 16:22:23.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:23.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:23.349][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-06-15 16:22:23.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-15 16:22:23.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:23.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:23.357][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-15 16:22:23.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-15 16:22:23.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:23.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:23.364][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-15 16:22:23.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-15 16:22:23.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:23.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:23.371][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-15 16:22:23.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-15 16:22:23.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:23.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:23.379][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-06-15 16:22:23.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-15 16:22:23.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:23.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:23.414][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-15 16:22:23.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-15 16:22:23.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:23.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:23.423][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-15 16:22:23.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-15 16:22:23.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:23.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:23.533][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-15 16:22:23.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-15 16:22:23.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:23.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:23.542][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-15 16:22:23.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-15 16:22:23.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:23.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:23.550][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-15 16:22:23.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-15 16:22:23.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:23.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:23.559][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-15 16:22:23.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-15 16:22:23.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:23.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:23.566][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-15 16:22:23.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-15 16:22:23.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:23.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:23.574][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-15 16:22:23.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-15 16:22:23.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:23.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:23.582][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-15 16:22:23.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-15 16:22:23.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:23.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:23.588][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-15 16:22:23.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-15 16:22:23.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:23.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:23.595][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-15 16:22:23.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-15 16:22:23.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:23.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:23.603][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-15 16:22:23.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-15 16:22:23.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:23.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:23.609][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-15 16:22:23.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-15 16:22:23.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:23.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:23.614][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-15 16:22:23.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-15 16:22:23.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:23.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:23.619][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-15 16:22:23.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-15 16:22:23.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:23.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-15 16:22:23.624][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 1.1.1.1.
biodb.TRACE[2024-06-15 16:22:23.627][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-15 16:22:23.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-15 16:22:23.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:23.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:23.632][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-15 16:22:23.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-15 16:22:23.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:23.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:23.638][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-15 16:22:23.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-15 16:22:23.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:23.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:23.643][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-15 16:22:23.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-15 16:22:23.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:23.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:23.943][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-15 16:22:23.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-15 16:22:23.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:23.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:23.969][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-15 16:22:23.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-15 16:22:23.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:23.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:23.981][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-15 16:22:23.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-15 16:22:23.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:23.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:23.986][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-15 16:22:23.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-15 16:22:23.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:23.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:23.997][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-15 16:22:23.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-15 16:22:24.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:24.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:24.004][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-15 16:22:24.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-15 16:22:24.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:24.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:24.009][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-15 16:22:24.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-15 16:22:24.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:24.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:24.014][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-15 16:22:24.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-15 16:22:24.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:24.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:24.019][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-15 16:22:24.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-15 16:22:24.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:24.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:24.024][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-15 16:22:24.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-15 16:22:24.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:24.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:24.029][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-15 16:22:24.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-15 16:22:24.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:24.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:24.047][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-15 16:22:24.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-15 16:22:24.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:24.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:24.055][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-15 16:22:24.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-15 16:22:24.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:24.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:24.062][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-15 16:22:24.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-15 16:22:24.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:24.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:24.070][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-15 16:22:24.072][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-15 16:22:24.073][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:24.075][ef$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:24.077][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-15 16:22:24.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-15 16:22:24.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:24.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:24.099][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-15 16:22:24.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-15 16:22:24.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:24.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:24.108][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-15 16:22:24.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-15 16:22:24.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:24.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:24.115][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-15 16:22:24.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-15 16:22:24.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:24.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:24.122][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-15 16:22:24.124][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-15 16:22:24.126][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:24.128][ef$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:24.130][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-15 16:22:24.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-15 16:22:24.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:24.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:24.150][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-15 16:22:24.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-15 16:22:24.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:24.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:24.156][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-15 16:22:24.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-15 16:22:24.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:24.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:24.161][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-15 16:22:24.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-15 16:22:24.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:24.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:24.166][ef$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-15 16:22:24.167][ef$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-15 16:22:24.168][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:24.170][ef$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:24.171][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-15 16:22:24.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-15 16:22:24.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:24.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:24.193][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-15 16:22:24.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-15 16:22:24.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:24.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:24.202][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-15 16:22:24.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-15 16:22:24.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:24.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:24.210][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-15 16:22:24.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-15 16:22:24.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:24.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:24.218][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-15 16:22:24.220][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-15 16:22:24.222][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:24.223][ef$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:24.225][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-15 16:22:24.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-15 16:22:24.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:24.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:24.256][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-15 16:22:24.259][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-15 16:22:24.261][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:24.263][ef$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:24.273][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-15 16:22:24.276][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-15 16:22:24.278][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:24.279][ef$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:24.290][ef$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-15 16:22:24.292][ef$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-15 16:22:24.294][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:24.296][ef$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:24.307][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-15 16:22:24.309][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-15 16:22:24.311][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:24.313][ef$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:24.345][loadFileContents] Loaded 1 files from cache: [1]: "F:/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/testref/entry-expasy.enzyme-1.1.1.54-content.txt".
biodb.DEBUG[2024-06-15 16:22:24.410][biodb$getFactory()$createEntryFromCo ...] Creating Expasy ENZYME database. entries from 1 content(s).
biodb.DEBUG[2024-06-15 16:22:24.413][biodb$getFactory()$createEntryFromCo ...] Parsing 1 Expasy ENZYME database. entries.
biodb.DEBUG[2024-06-15 16:22:24.417][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-15 16:22:24.419][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-15 16:22:24.422][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-15 16:22:24.435][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:22:24.438][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:22:24.439][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:24.441][FUN] Functions in observer BiodbConfig: [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[2024-06-15 16:22:24.445][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-15 16:22:24.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-15 16:22:24.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:24.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:24.453][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-15 16:22:24.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-15 16:22:24.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:24.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:24.462][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-15 16:22:24.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-15 16:22:24.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:24.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:24.470][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-06-15 16:22:24.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-15 16:22:24.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:24.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:24.478][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-15 16:22:24.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-15 16:22:24.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:24.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:24.486][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-15 16:22:24.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-15 16:22:24.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:24.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:24.493][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-15 16:22:24.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-15 16:22:24.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:24.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:24.501][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-15 16:22:24.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-15 16:22:24.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:24.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:24.517][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-15 16:22:24.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-15 16:22:24.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:24.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:24.525][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-15 16:22:24.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-15 16:22:24.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:24.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:24.533][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-15 16:22:24.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-15 16:22:24.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:24.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:24.542][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-15 16:22:24.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-15 16:22:24.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:24.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:24.550][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-15 16:22:24.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-15 16:22:24.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:24.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:24.558][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-15 16:22:24.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-15 16:22:24.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:24.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-15 16:22:24.564][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 1.1.1.54.
biodb.TRACE[2024-06-15 16:22:24.592][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-15 16:22:24.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-15 16:22:24.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:24.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:24.599][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-15 16:22:24.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-15 16:22:24.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:24.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:24.606][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-15 16:22:24.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-15 16:22:24.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:24.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:24.613][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-15 16:22:24.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-15 16:22:24.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:24.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:24.622][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-15 16:22:24.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-15 16:22:24.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:24.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:24.639][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-15 16:22:24.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-15 16:22:24.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:24.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:24.657][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-15 16:22:24.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-15 16:22:24.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:24.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:24.666][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-15 16:22:24.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-15 16:22:24.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:24.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:24.673][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-15 16:22:24.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-15 16:22:24.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:24.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:24.684][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-15 16:22:24.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-15 16:22:24.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:24.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:24.692][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-15 16:22:24.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-15 16:22:24.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:24.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:24.699][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-15 16:22:24.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-15 16:22:24.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:24.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:24.704][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-15 16:22:24.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-15 16:22:24.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:24.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:24.712][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-15 16:22:24.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-15 16:22:24.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:24.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:24.719][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-15 16:22:24.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-15 16:22:24.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:24.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:24.756][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-15 16:22:24.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-15 16:22:24.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:24.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:24.765][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-15 16:22:24.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-15 16:22:24.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:24.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:24.772][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-15 16:22:24.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-15 16:22:24.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:24.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:24.777][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-15 16:22:24.778][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-15 16:22:24.779][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:24.781][ef$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:24.782][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-15 16:22:24.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-15 16:22:24.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:24.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:24.801][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-15 16:22:24.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-15 16:22:24.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:24.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:24.809][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-15 16:22:24.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-15 16:22:24.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:24.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:24.816][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-15 16:22:24.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-15 16:22:24.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:24.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:24.823][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-15 16:22:24.825][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-15 16:22:24.827][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:24.828][ef$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:24.830][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-15 16:22:24.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-15 16:22:24.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:24.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:24.854][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-15 16:22:24.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-15 16:22:24.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:24.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:24.860][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-15 16:22:24.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-15 16:22:24.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:24.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:24.866][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-15 16:22:24.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-15 16:22:24.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:24.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:24.871][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-15 16:22:24.873][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-15 16:22:24.874][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:24.875][ef$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:24.877][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-15 16:22:24.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-15 16:22:24.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:24.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:24.892][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-15 16:22:24.894][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-15 16:22:24.895][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:24.896][ef$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:24.904][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-15 16:22:24.905][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-15 16:22:24.906][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:24.907][ef$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:24.914][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-15 16:22:24.916][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-15 16:22:24.917][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:24.918][ef$get] fields variable is a list.
biodb.INFO [2024-06-15 16:22:24.931][biodb::testThat]
biodb.INFO [2024-06-15 16:22:24.932][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-06-15 16:22:24.934][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-15 16:22:24.936][biodb::testThat]
biodb.DEBUG[2024-06-15 16:22:24.939][private$loadEntries] Creating entries from ids [2]: "1.1.1.1, 1.1.1.54".
biodb.DEBUG[2024-06-15 16:22:24.945][conn$getEntryContent] Get Expasy ENZYME database. entry content(s) for 2 id(s)...
biodb.TRACE[2024-06-15 16:22:24.955][cch$loadFileContent] Trying to load 2 files from cache: [2]: "1.1.1.1, 1.1.1.54".
biodb.INFO [2024-06-15 16:22:24.957][self$getFolderPath] Create cache folder "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280" for "expasy.enzyme-b59b84d962b6741050ba8f70ff4db280".
biodb.TRACE[2024-06-15 16:22:24.958][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2024-06-15 16:22:24.960][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-15 16:22:24.961][conn$getEntryContent] 0 Expasy ENZYME database. entry content(s) loaded from cache.
biodb.DEBUG[2024-06-15 16:22:24.963][conn$getEntryContent] 2 entry content(s) need to be fetched from Expasy ENZYME database. database "https://enzyme.expasy.org/".
biodb.DEBUG[2024-06-15 16:22:24.964][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-15 16:22:24.965][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-15 16:22:24.970][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-15 16:22:24.972][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-15 16:22:24.973][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-15 16:22:24.980][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:22:24.988][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:22:24.989][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:24.990][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:22:24.992][scheduler$sendRequest] Getting content of get URL request "https://enzyme.expasy.org/EC/1.1.1.1.txt".
biodb.DEBUG[2024-06-15 16:22:25.014][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-15 16:22:25.016][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-15 16:22:25.017][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/EC/1.1.1.1.txt".
biodb.TRACE[2024-06-15 16:22:25.928][doesRCurlRequestUrlExist] According to RCurl, URL https://enzyme.expasy.org/EC/1.1.1.1.txt does not exist.
biodb.TRACE[2024-06-15 16:22:25.930][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-15 16:22:25.932][getUrlRequestResult] URL "https://enzyme.expasy.org/EC/1.1.1.1.txt" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-15 16:22:25.934][getBaseUrlRequestResult] Using base::url() for sending request (https://enzyme.expasy.org/EC/1.1.1.1.txt).
biodb.DEBUG[2024-06-15 16:22:26.348][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-15 16:22:26.353][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a52675cfd2f0c2b41556caa64d9341e3.content"
biodb.TRACE[2024-06-15 16:22:26.379][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a52675cfd2f0c2b41556caa64d9341e3.request"
biodb.DEBUG[2024-06-15 16:22:26.384][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-15 16:22:26.385][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-15 16:22:26.387][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-15 16:22:26.398][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:22:26.400][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:22:26.401][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:26.403][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:22:26.434][scheduler$sendRequest] Getting content of get URL request "https://enzyme.expasy.org/EC/1.1.1.54.txt".
biodb.DEBUG[2024-06-15 16:22:26.452][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-15 16:22:26.455][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-15 16:22:26.486][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/EC/1.1.1.54.txt".
biodb.TRACE[2024-06-15 16:22:26.705][doesRCurlRequestUrlExist] According to RCurl, URL https://enzyme.expasy.org/EC/1.1.1.54.txt does not exist.
biodb.TRACE[2024-06-15 16:22:26.707][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-15 16:22:26.709][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[2024-06-15 16:22:26.711][getBaseUrlRequestResult] Using base::url() for sending request (https://enzyme.expasy.org/EC/1.1.1.54.txt).
biodb.DEBUG[2024-06-15 16:22:27.113][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-15 16:22:27.117][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a9b93566a091cbe35a06e4b3871f95c9.content"
biodb.TRACE[2024-06-15 16:22:27.124][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a9b93566a091cbe35a06e4b3871f95c9.request"
biodb.TRACE[2024-06-15 16:22:27.129][private$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[2024-06-15 16:22:27.133][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-15 16:22:27.136][self$createEntryFromContent] Creating Expasy ENZYME database. entries from 2 content(s).
biodb.DEBUG[2024-06-15 16:22:27.138][self$createEntryFromContent] Parsing 2 Expasy ENZYME database. entries.
biodb.DEBUG[2024-06-15 16:22:27.142][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-15 16:22:27.143][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-15 16:22:27.145][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-15 16:22:27.155][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:22:27.157][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:22:27.159][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:27.161][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-15 16:22:27.166][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-15 16:22:27.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-15 16:22:27.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:27.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:27.174][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-15 16:22:27.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-15 16:22:27.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:27.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:27.183][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-15 16:22:27.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-15 16:22:27.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:27.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:27.191][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-06-15 16:22:27.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-15 16:22:27.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:27.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:27.199][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-15 16:22:27.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-15 16:22:27.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:27.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:27.207][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-15 16:22:27.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-15 16:22:27.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:27.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:27.215][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-15 16:22:27.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-15 16:22:27.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:27.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:27.220][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-15 16:22:27.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-15 16:22:27.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:27.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:27.227][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-15 16:22:27.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-15 16:22:27.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:27.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:27.235][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-15 16:22:27.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-15 16:22:27.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:27.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:27.242][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-15 16:22:27.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-15 16:22:27.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:27.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:27.249][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-15 16:22:27.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-15 16:22:27.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:27.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:27.258][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-15 16:22:27.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-15 16:22:27.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:27.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:27.266][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-15 16:22:27.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-15 16:22:27.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:27.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:27.275][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-15 16:22:27.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-15 16:22:27.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:27.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:27.284][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-15 16:22:27.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-15 16:22:27.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:27.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-15 16:22:27.291][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-15 16:22:27.293][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-15 16:22:27.294][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-15 16:22:27.315][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:22:27.317][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:22:27.319][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:27.320][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-15 16:22:27.324][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-15 16:22:27.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-15 16:22:27.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:27.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:27.331][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-15 16:22:27.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-15 16:22:27.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:27.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:27.337][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-15 16:22:27.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-15 16:22:27.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:27.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:27.342][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-06-15 16:22:27.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-15 16:22:27.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:27.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:27.348][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-15 16:22:27.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-15 16:22:27.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:27.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:27.356][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-15 16:22:27.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-15 16:22:27.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:27.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:27.364][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-15 16:22:27.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-15 16:22:27.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:27.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:27.371][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-15 16:22:27.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-15 16:22:27.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:27.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:27.379][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-15 16:22:27.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-15 16:22:27.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:27.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:27.387][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-15 16:22:27.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-15 16:22:27.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:27.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:27.395][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-15 16:22:27.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-15 16:22:27.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:27.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:27.403][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-15 16:22:27.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-15 16:22:27.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:27.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:27.411][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-15 16:22:27.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-15 16:22:27.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:27.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:27.419][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-15 16:22:27.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-15 16:22:27.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:27.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:27.427][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-15 16:22:27.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-15 16:22:27.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:27.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:27.435][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-15 16:22:27.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-15 16:22:27.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:27.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:27.442][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-15 16:22:27.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-15 16:22:27.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:27.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-15 16:22:27.450][self$createEntryFromContent] Accession numbers: 1.1.1.1, 1.1.1.54.
biodb.TRACE[2024-06-15 16:22:27.452][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-06-15 16:22:27.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-06-15 16:22:27.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:27.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:27.460][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-06-15 16:22:27.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-06-15 16:22:27.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:27.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:27.467][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-06-15 16:22:27.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-06-15 16:22:27.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:27.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:27.486][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-06-15 16:22:27.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-06-15 16:22:27.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:27.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:27.495][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-06-15 16:22:27.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-06-15 16:22:27.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:27.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:27.504][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-06-15 16:22:27.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-06-15 16:22:27.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:27.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-15 16:22:27.538][biodb::testThat]
biodb.INFO [2024-06-15 16:22:27.540][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-06-15 16:22:27.543][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-15 16:22:27.545][biodb::testThat]
biodb.TRACE[2024-06-15 16:22:27.551][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-15 16:22:27.553][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-15 16:22:27.555][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:27.557][ef$get] fields variable is a list.
biodb.DEBUG[2024-06-15 16:22:27.559][function(conn, opt)] Testing searchForEntries() with entry "1.1.1.1" and field "name".
biodb.TRACE[2024-06-15 16:22:27.606][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-15 16:22:27.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-15 16:22:27.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:27.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:27.614][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-15 16:22:27.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-15 16:22:27.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:27.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:27.622][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-15 16:22:27.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-15 16:22:27.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:27.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-15 16:22:27.634][function(conn, opt)] With value "alcohol dehydrogenase".
biodb.DEBUG[2024-06-15 16:22:27.638][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://enzyme.expasy.org/enzyme-byname.html?alcohol dehydrogenase".
biodb.DEBUG[2024-06-15 16:22:27.643][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-15 16:22:27.645][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-15 16:22:27.647][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase".
biodb.TRACE[2024-06-15 16:22:27.874][doesRCurlRequestUrlExist] According to RCurl, URL https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase does not exist.
biodb.TRACE[2024-06-15 16:22:27.876][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-15 16:22:27.878][getUrlRequestResult] URL "https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-15 16:22:27.880][getBaseUrlRequestResult] Using base::url() for sending request (https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase).
biodb.DEBUG[2024-06-15 16:22:28.310][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-15 16:22:28.314][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.content"
biodb.TRACE[2024-06-15 16:22:28.321][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.request"
biodb.DEBUG[2024-06-15 16:22:28.330][function(conn, opt)] With found IDs [1]: "1.1.1.1".
biodb.INFO [2024-06-15 16:22:28.364][biodb::testThat]
biodb.INFO [2024-06-15 16:22:28.366][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-06-15 16:22:28.368][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-15 16:22:28.370][biodb::testThat]
biodb.TRACE[2024-06-15 16:22:28.420][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-15 16:22:28.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-15 16:22:28.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:28.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:28.428][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-15 16:22:28.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-15 16:22:28.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:28.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:28.435][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-15 16:22:28.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-15 16:22:28.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:28.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-15 16:22:28.482][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://enzyme.expasy.org/enzyme-byname.html?alcohol dehydrogenase".
biodb.DEBUG[2024-06-15 16:22:28.487][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-15 16:22:28.509][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f603fa2a57aec59588edc37541c6f6d5".
biodb.TRACE[2024-06-15 16:22:28.512][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-15 16:22:28.518][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.content".
biodb.INFO [2024-06-15 16:22:28.556][biodb::testThat]
biodb.INFO [2024-06-15 16:22:28.558][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-06-15 16:22:28.560][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-15 16:22:28.562][biodb::testThat]
biodb.TRACE[2024-06-15 16:22:28.592][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-15 16:22:28.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-15 16:22:28.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:28.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:28.602][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-15 16:22:28.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-15 16:22:28.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:28.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:28.610][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-15 16:22:28.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-15 16:22:28.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:28.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:28.618][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-15 16:22:28.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-15 16:22:28.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:28.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:28.680][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-15 16:22:28.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-15 16:22:28.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:28.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:28.689][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-15 16:22:28.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-15 16:22:28.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:28.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:28.698][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-15 16:22:28.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-15 16:22:28.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:28.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:28.707][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-15 16:22:28.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-15 16:22:28.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:28.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-15 16:22:28.729][biodb::testThat]
biodb.INFO [2024-06-15 16:22:28.731][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-06-15 16:22:28.734][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-15 16:22:28.736][biodb::testThat]
biodb.INFO [2024-06-15 16:22:28.757][biodb::testThat]
biodb.INFO [2024-06-15 16:22:28.760][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-06-15 16:22:28.762][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-15 16:22:28.764][biodb::testThat]
biodb.INFO [2024-06-15 16:22:28.793][biodb::testThat]
biodb.INFO [2024-06-15 16:22:28.795][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-06-15 16:22:28.796][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-15 16:22:28.798][biodb::testThat]
biodb.DEBUG[2024-06-15 16:22:28.819][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[2024-06-15 16:22:29.036][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 [2024-06-15 16:22:29.479][biodb::testThat]
biodb.INFO [2024-06-15 16:22:29.482][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-06-15 16:22:29.483][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-15 16:22:29.485][biodb::testThat]
biodb.DEBUG[2024-06-15 16:22:29.710][getUrlContent] Use base::url() for downloading content of URL https://enzyme.expasy.org/images/1.1.1.1/image.png.
biodb.TRACE[2024-06-15 16:22:30.158][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-15 16:22:30.160][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-15 16:22:30.162][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:30.164][ef$get] fields variable is a list.
biodb.TRACE[2024-06-15 16:22:30.166][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-15 16:22:30.168][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-15 16:22:30.170][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-15 16:22:30.172][ef$get] fields variable is a list.
biodb.INFO [2024-06-15 16:22:30.174][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-06-15 16:22:30.176][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector expasy.enzyme from the request scheduler
biodb.INFO [2024-06-15 16:22:30.178][self$deleteConn] Connector "expasy.enzyme" deleted.
biodb.DEBUG[2024-06-15 16:22:30.180][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-06-15 16:22:30.181][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-15 16:22:30.183][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-15 16:22:30.185][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:22:30.186][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:22:30.187][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:30.188][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-06-15 16:22:30.199][biodb::testContext]
biodb.INFO [2024-06-15 16:22:30.201][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-15 16:22:30.202][biodb::testContext] Test context - Example long tests
biodb.INFO [2024-06-15 16:22:30.203][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-15 16:22:30.204][biodb::testContext]
biodb.INFO [2024-06-15 16:22:30.208][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.13.0.
biodb.DEBUG[2024-06-15 16:22:30.212][self$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.20-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2024-06-15 16:22:30.220][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-15 16:22:30.221][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-06-15 16:22:30.223][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-06-15 16:22:30.225][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:30.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:30.228][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:22:30.239][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-06-15 16:22:30.242][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-06-15 16:22:30.244][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:30.246][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:30.248][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:22:30.250][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-06-15 16:22:30.252][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-06-15 16:22:30.254][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:30.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:30.257][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:22:30.259][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-06-15 16:22:30.260][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-06-15 16:22:30.262][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-06-15 16:22:30.264][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:30.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:30.268][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:22:30.270][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-06-15 16:22:30.272][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-06-15 16:22:30.274][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-06-15 16:22:30.276][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:30.277][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:30.279][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:22:30.281][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-06-15 16:22:30.282][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-06-15 16:22:30.284][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:30.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:30.288][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:22:30.289][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-06-15 16:22:30.290][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-06-15 16:22:30.292][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-06-15 16:22:30.293][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:30.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:30.295][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:22:30.297][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-06-15 16:22:30.300][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-06-15 16:22:30.302][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:30.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:30.305][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:22:30.307][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-06-15 16:22:30.309][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-06-15 16:22:30.312][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-06-15 16:22:30.313][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:30.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:30.317][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:22:30.319][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-06-15 16:22:30.321][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-06-15 16:22:30.323][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-06-15 16:22:30.325][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-06-15 16:22:30.327][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-06-15 16:22:30.329][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-06-15 16:22:30.331][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:30.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:30.334][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:22:30.337][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-06-15 16:22:30.339][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-06-15 16:22:30.340][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:30.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:30.344][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:22:30.346][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-06-15 16:22:30.348][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-06-15 16:22:30.350][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:30.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:30.354][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:22:30.356][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-06-15 16:22:30.358][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-06-15 16:22:30.360][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:30.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:30.364][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:22:30.366][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-06-15 16:22:30.367][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-06-15 16:22:30.369][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:30.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:30.371][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:22:30.372][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-06-15 16:22:30.374][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-06-15 16:22:30.375][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:30.376][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:30.377][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:22:30.378][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-06-15 16:22:30.380][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-06-15 16:22:30.384][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-06-15 16:22:30.385][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:30.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:30.388][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:22:30.390][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-06-15 16:22:30.392][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-06-15 16:22:30.394][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-06-15 16:22:30.395][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:30.396][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:30.397][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:22:30.399][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-06-15 16:22:30.432][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-15 16:22:30.434][self$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[2024-06-15 16:22:30.435][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-15 16:22:30.436][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-15 16:22:30.438][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-15 16:22:30.439][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-15 16:22:30.440][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-15 16:22:30.442][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-15 16:22:30.443][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-15 16:22:30.445][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-15 16:22:30.446][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-15 16:22:30.447][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-06-15 16:22:30.448][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-15 16:22:30.450][self$setPropertyValue]
biodb.DEBUG[2024-06-15 16:22:30.451][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-15 16:22:30.452][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-15 16:22:30.452][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-15 16:22:30.452][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-15 16:22:30.452][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-15 16:22:30.452][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-15 16:22:30.453][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-15 16:22:30.455][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-15 16:22:30.456][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-15 16:22:30.457][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-15 16:22:30.458][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-15 16:22:30.459][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-15 16:22:30.461][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-15 16:22:30.462][self$setPropertyValue]
biodb.DEBUG[2024-06-15 16:22:30.463][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-15 16:22:30.464][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-15 16:22:30.465][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-15 16:22:30.467][self$setPropertyValue]
biodb.DEBUG[2024-06-15 16:22:30.469][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-06-15 16:22:30.471][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-15 16:22:30.472][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-06-15 16:22:30.473][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-15 16:22:30.474][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-15 16:22:30.476][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-15 16:22:30.477][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-15 16:22:30.478][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-15 16:22:30.480][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-15 16:22:30.482][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-15 16:22:30.483][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-15 16:22:30.485][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-15 16:22:30.487][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-06-15 16:22:30.489][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-15 16:22:30.491][self$setPropertyValue]
biodb.DEBUG[2024-06-15 16:22:30.493][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-15 16:22:30.494][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-15 16:22:30.494][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-15 16:22:30.494][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-15 16:22:30.494][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-15 16:22:30.494][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-15 16:22:30.496][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-15 16:22:30.497][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-15 16:22:30.498][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-15 16:22:30.499][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-15 16:22:30.500][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-15 16:22:30.501][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-15 16:22:30.503][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-15 16:22:30.504][self$setPropertyValue]
biodb.DEBUG[2024-06-15 16:22:30.505][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-15 16:22:30.506][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-15 16:22:30.508][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-15 16:22:30.509][self$setPropertyValue]
biodb.DEBUG[2024-06-15 16:22:30.510][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-06-15 16:22:30.512][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-15 16:22:30.513][self$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[2024-06-15 16:22:30.515][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-15 16:22:30.516][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-15 16:22:30.517][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-15 16:22:30.518][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-15 16:22:30.520][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-15 16:22:30.521][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-15 16:22:30.522][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-15 16:22:30.523][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-15 16:22:30.524][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-15 16:22:30.526][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-06-15 16:22:30.528][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-15 16:22:30.530][self$setPropertyValue]
biodb.DEBUG[2024-06-15 16:22:30.539][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-15 16:22:30.541][self$setPropertyValue]
biodb.DEBUG[2024-06-15 16:22:30.542][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-15 16:22:30.543][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-15 16:22:30.544][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-15 16:22:30.546][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-15 16:22:30.547][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-15 16:22:30.549][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-15 16:22:30.551][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-15 16:22:30.553][self$setPropertyValue]
biodb.DEBUG[2024-06-15 16:22:30.555][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-15 16:22:30.556][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-15 16:22:30.558][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-15 16:22:30.560][self$setPropertyValue]
biodb.DEBUG[2024-06-15 16:22:30.563][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-06-15 16:22:30.566][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-15 16:22:30.568][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-06-15 16:22:30.570][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-15 16:22:30.571][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-15 16:22:30.573][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-15 16:22:30.575][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-15 16:22:30.577][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-15 16:22:30.579][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-15 16:22:30.581][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-15 16:22:30.583][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-15 16:22:30.585][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-15 16:22:30.587][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-06-15 16:22:30.588][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-15 16:22:30.589][self$setPropertyValue]
biodb.DEBUG[2024-06-15 16:22:30.591][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-15 16:22:30.593][self$setPropertyValue]
biodb.DEBUG[2024-06-15 16:22:30.595][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-15 16:22:30.597][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-15 16:22:30.599][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-15 16:22:30.601][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-15 16:22:30.603][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-15 16:22:30.604][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-15 16:22:30.606][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-15 16:22:30.608][self$setPropertyValue]
biodb.DEBUG[2024-06-15 16:22:30.610][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-15 16:22:30.612][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-15 16:22:30.614][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-15 16:22:30.615][self$setPropertyValue]
biodb.DEBUG[2024-06-15 16:22:30.617][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-15 16:22:30.619][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:30.621][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:22:30.623][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:30.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:22:30.626][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:22:30.628][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:30.630][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:22:30.632][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:30.634][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:22:30.636][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:22:30.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:30.640][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:22:30.642][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:30.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:22:30.646][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:22:30.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:30.650][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:22:30.652][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:30.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:22:30.655][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:22:30.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:30.659][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[2024-06-15 16:22:30.661][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:30.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:22:30.665][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:22:30.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:30.669][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:22:30.671][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:30.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:22:30.675][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:22:30.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:30.678][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:22:30.680][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:30.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:22:30.684][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:22:30.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:30.688][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:22:30.690][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:30.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:22:30.694][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:22:30.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:30.697][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:22:30.699][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:30.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:22:30.703][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:22:30.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:30.707][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:22:30.709][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:30.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:22:30.713][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:22:30.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:30.717][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:22:30.719][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:30.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:22:30.722][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:22:30.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:30.726][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:22:30.728][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:30.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:22:30.741][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:22:30.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:30.745][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:22:30.747][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:30.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:22:30.751][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:22:30.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:30.754][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:22:30.756][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:30.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:22:30.760][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:22:30.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:30.764][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:22:30.766][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:30.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:22:30.770][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:22:30.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:30.774][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:22:30.775][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:30.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:22:30.779][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:22:30.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:30.783][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:22:30.785][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:30.787][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:22:30.789][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:22:30.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:30.792][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:22:30.795][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-06-15 16:22:30.797][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-06-15 16:22:30.800][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-06-15 16:22:30.803][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-06-15 16:22:30.806][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-15 16:22:30.809][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-15 16:22:30.811][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-06-15 16:22:30.814][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-06-15 16:22:30.817][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-15 16:22:30.820][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-15 16:22:30.822][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-15 16:22:30.825][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-06-15 16:22:30.828][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-06-15 16:22:30.831][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-06-15 16:22:30.833][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-06-15 16:22:30.836][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-15 16:22:30.839][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-06-15 16:22:30.842][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-06-15 16:22:30.844][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-15 16:22:30.847][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-06-15 16:22:30.850][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-06-15 16:22:30.852][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-06-15 16:22:30.855][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-06-15 16:22:30.858][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-06-15 16:22:30.860][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-06-15 16:22:30.863][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-06-15 16:22:30.866][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-06-15 16:22:30.869][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-06-15 16:22:30.872][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-06-15 16:22:30.874][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-06-15 16:22:30.877][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-06-15 16:22:30.880][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-06-15 16:22:30.883][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-06-15 16:22:30.885][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-06-15 16:22:30.888][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-06-15 16:22:30.891][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-06-15 16:22:30.894][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-06-15 16:22:30.896][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-06-15 16:22:30.899][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-06-15 16:22:30.902][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-06-15 16:22:30.904][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-06-15 16:22:30.907][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-06-15 16:22:30.910][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-06-15 16:22:30.913][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-06-15 16:22:30.916][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-06-15 16:22:30.919][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-06-15 16:22:30.921][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-06-15 16:22:30.924][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-06-15 16:22:30.927][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-06-15 16:22:30.938][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-06-15 16:22:30.941][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-06-15 16:22:30.944][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-06-15 16:22:30.947][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-06-15 16:22:30.950][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-06-15 16:22:30.953][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-06-15 16:22:30.955][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-06-15 16:22:30.958][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-06-15 16:22:30.961][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-06-15 16:22:30.963][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-06-15 16:22:30.966][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-06-15 16:22:30.969][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-06-15 16:22:30.971][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-06-15 16:22:30.974][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-06-15 16:22:30.977][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-06-15 16:22:30.980][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-06-15 16:22:30.982][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-06-15 16:22:30.985][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-15 16:22:30.988][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-15 16:22:30.991][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-06-15 16:22:30.993][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-06-15 16:22:30.996][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-06-15 16:22:30.999][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-06-15 16:22:31.001][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-06-15 16:22:31.004][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-06-15 16:22:31.007][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-06-15 16:22:31.010][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-06-15 16:22:31.012][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-06-15 16:22:31.015][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-06-15 16:22:31.018][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-06-15 16:22:31.021][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-06-15 16:22:31.024][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-06-15 16:22:31.026][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-06-15 16:22:31.029][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-06-15 16:22:31.032][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-06-15 16:22:31.037][initialize] This is biodb version 1.13.0.
biodb.DEBUG[2024-06-15 16:22:31.039][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-15 16:22:31.041][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:22:31.043][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:22:31.045][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:31.046][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:22:31.048][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:31.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-15 16:22:31.052][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-15 16:22:31.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:22:31.056][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:22:31.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:31.060][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:22:31.062][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:31.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-15 16:22:31.065][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-15 16:22:31.067][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:22:31.069][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:22:31.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:31.073][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:22:31.075][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:31.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-15 16:22:31.079][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-15 16:22:31.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:22:31.082][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:22:31.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:31.086][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:22:31.088][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:31.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-15 16:22:31.092][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-15 16:22:31.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:22:31.096][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:22:31.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:31.099][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:22:31.101][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:31.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-15 16:22:31.105][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-15 16:22:31.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:22:31.109][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:22:31.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:31.113][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:22:31.114][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:31.116][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-15 16:22:31.118][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-15 16:22:31.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:22:31.122][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:22:31.123][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:31.124][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:22:31.126][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:31.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-15 16:22:31.134][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-15 16:22:31.135][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:22:31.136][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:22:31.137][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:31.139][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:22:31.140][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:31.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-15 16:22:31.142][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-15 16:22:31.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:22:31.145][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:22:31.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:31.147][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:22:31.148][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:31.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-15 16:22:31.150][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-15 16:22:31.151][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:22:31.153][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:22:31.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:31.155][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:22:31.156][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:31.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-15 16:22:31.158][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-15 16:22:31.160][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:22:31.161][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:22:31.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:31.163][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:22:31.164][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:31.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-15 16:22:31.167][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-15 16:22:31.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:22:31.169][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:22:31.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:31.172][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:22:31.173][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:31.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-15 16:22:31.176][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-15 16:22:31.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:22:31.178][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:22:31.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:31.180][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:22:31.181][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:31.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-15 16:22:31.183][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-15 16:22:31.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:22:31.186][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:22:31.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:31.188][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:22:31.190][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:31.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-15 16:22:31.192][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-15 16:22:31.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:22:31.194][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:22:31.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:31.196][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:22:31.197][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:31.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-15 16:22:31.200][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-15 16:22:31.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:22:31.202][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:22:31.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:31.204][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:22:31.206][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:31.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-15 16:22:31.209][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-15 16:22:31.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:22:31.213][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:22:31.214][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:31.215][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-15 16:22:31.216][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-15 16:22:31.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-15 16:22:31.219][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-15 16:22:31.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:22:31.221][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:22:31.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:31.223][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[2024-06-15 16:22:31.228][biodb$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/definitions.yml".
biodb.DEBUG[2024-06-15 16:22:31.230][self$getDbsInfo()$define] Define connector expasy.enzyme.
biodb.DEBUG[2024-06-15 16:22:31.233][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-15 16:22:31.235][self$setPropertyValue] Setting property "description" to "Write here the description of this database.".
biodb.DEBUG[2024-06-15 16:22:31.237][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-15 16:22:31.239][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-15 16:22:31.241][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-15 16:22:31.243][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-15 16:22:31.245][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-06-15 16:22:31.247][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-15 16:22:31.249][self$setPropertyValue] Setting property "entry.content.type" to "txt".
biodb.DEBUG[2024-06-15 16:22:31.251][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-15 16:22:31.254][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-15 16:22:31.256][self$setPropertyValue] Setting property "name" to "Expasy ENZYME database.".
biodb.DEBUG[2024-06-15 16:22:31.258][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-15 16:22:31.260][self$setPropertyValue] Setting property "parsing.expr" to "^ID\s+([0-9.]+)$".
biodb.DEBUG[2024-06-15 16:22:31.260][self$setPropertyValue] Setting property "parsing.expr" to "^CA\s+(.+?)\.?$".
biodb.DEBUG[2024-06-15 16:22:31.260][self$setPropertyValue] Setting property "parsing.expr" to "^CF\s+(.+?)\.?$".
biodb.DEBUG[2024-06-15 16:22:31.260][self$setPropertyValue] Setting property "parsing.expr" to "^DE\s+(.+?)\.?$".
biodb.DEBUG[2024-06-15 16:22:31.262][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-06-15 16:22:31.263][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-15 16:22:31.264][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-06-15 16:22:31.266][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-15 16:22:31.267][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-15 16:22:31.268][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-15 16:22:31.269][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-15 16:22:31.270][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-15 16:22:31.271][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-15 16:22:31.273][self$setPropertyValue] Setting property "urls" to "https://enzyme.expasy.org/".
biodb.DEBUG[2024-06-15 16:22:31.279][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-15 16:22:31.281][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-15 16:22:31.282][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-06-15 16:22:31.283][self$setPropertyValue]
biodb.DEBUG[2024-06-15 16:22:31.285][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-15 16:22:31.288][super$initialize] Initialize connector expasy.enzyme.
biodb.DEBUG[2024-06-15 16:22:31.289][super$initialize] Register connector expasy.enzyme with the request scheduler
biodb.DEBUG[2024-06-15 16:22:31.291][private$bdb$getRequestScheduler()$re ...] Register connector expasy.enzyme.
biodb.DEBUG[2024-06-15 16:22:31.293][private$addConnectorRules] Create new rule for URL "enzyme.expasy.org" of connector "expasy.enzyme".
biodb.DEBUG[2024-06-15 16:22:31.295][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-15 16:22:31.296][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-15 16:22:31.298][biodb$getFactory()$createConn] Creating new connector expasy.enzyme for database class expasy.enzyme .
biodb.INFO [2024-06-15 16:22:31.299][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-06-15 16:22:31.301][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector expasy.enzyme from the request scheduler
biodb.INFO [2024-06-15 16:22:31.302][self$deleteConn] Connector "expasy.enzyme" deleted.
biodb.DEBUG[2024-06-15 16:22:31.303][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-06-15 16:22:31.304][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-15 16:22:31.305][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-15 16:22:31.306][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-15 16:22:31.308][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-15 16:22:31.309][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-06-15 16:22:31.310][FUN] Functions in observer 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:
###
###   F:\biocbuild\bbs-3.20-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_1.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck'
* using R version 4.4.0 RC (2024-04-16 r86468 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 '1.9.0'
* 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
  'F:/biocbuild/bbs-3.20-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)