Back to Long Tests report for BioC 3.20

This page was generated on 2024-06-29 23:55 -0400 (Sat, 29 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4693
palomino6Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4408
lconwaymacOS 12.7.1 Montereyx86_644.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" 4407
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: 2024-06-29 09:55 -0400 (Sat, 29 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  
palomino6Windows Server 2022 Datacenter / x64  ERROR  
lconwaymacOS 12.7.1 Monterey / x86_64  ERROR  

CHECK results for biodbExpasy on palomino6

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: C:\Users\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: 2024-06-29 16:01:46 -0400 (Sat, 29 Jun 2024)
EndedAt: 2024-06-29 16:02:38 -0400 (Sat, 29 Jun 2024)
EllapsedTime: 52.1 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbExpasy.Rcheck
Warnings: NA

Tests output

biodbExpasy.Rcheck/tests/testthat.Rout.fail


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

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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 [2024-06-29 16:02:29.169][biodb::testContext]
biodb.INFO [2024-06-29 16:02:29.172][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-29 16:02:29.174][biodb::testContext] Test context - Generic long tests
biodb.INFO [2024-06-29 16:02:29.175][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-29 16:02:29.176][biodb::testContext]
biodb.INFO [2024-06-29 16:02:29.185][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.13.0.
biodb.DEBUG[2024-06-29 16:02:29.188][self$loadDefinitions] Load definitions from file "C:/Users/biocbuild/bbs-3.20-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2024-06-29 16:02:29.197][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-29 16:02:29.198][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-06-29 16:02:29.199][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-06-29 16:02:29.200][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:29.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:29.203][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:29.204][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-06-29 16:02:29.234][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-06-29 16:02:29.235][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:29.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:29.237][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:29.238][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-06-29 16:02:29.239][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-06-29 16:02:29.240][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:29.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:29.242][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:29.243][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-06-29 16:02:29.244][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-06-29 16:02:29.245][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-06-29 16:02:29.246][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:29.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:29.248][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[2024-06-29 16:02:29.249][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-06-29 16:02:29.250][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-06-29 16:02:29.251][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-06-29 16:02:29.252][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:29.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:29.253][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:29.255][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-06-29 16:02:29.256][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-06-29 16:02:29.257][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:29.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:29.258][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:29.259][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-06-29 16:02:29.260][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-06-29 16:02:29.262][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-06-29 16:02:29.262][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:29.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:29.264][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:29.265][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-06-29 16:02:29.266][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-06-29 16:02:29.267][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:29.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:29.269][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:29.270][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-06-29 16:02:29.271][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-06-29 16:02:29.272][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-06-29 16:02:29.273][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:29.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:29.275][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:29.276][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-06-29 16:02:29.277][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-06-29 16:02:29.278][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-06-29 16:02:29.279][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-06-29 16:02:29.280][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-06-29 16:02:29.281][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-06-29 16:02:29.282][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:29.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:29.284][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:29.285][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-06-29 16:02:29.286][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-06-29 16:02:29.287][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:29.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:29.289][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:29.290][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-06-29 16:02:29.291][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-06-29 16:02:29.292][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:29.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:29.294][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:29.295][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-06-29 16:02:29.296][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-06-29 16:02:29.297][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:29.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:29.299][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:29.300][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-06-29 16:02:29.301][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-06-29 16:02:29.302][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:29.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:29.304][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:29.305][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-06-29 16:02:29.306][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-06-29 16:02:29.307][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:29.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:29.309][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:29.310][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-06-29 16:02:29.311][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-06-29 16:02:29.315][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-06-29 16:02:29.316][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:29.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:29.318][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:29.319][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-06-29 16:02:29.320][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-06-29 16:02:29.321][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-06-29 16:02:29.322][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:29.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:29.324][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:29.327][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-06-29 16:02:29.354][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-29 16:02:29.367][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-06-29 16:02:29.369][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:29.370][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-29 16:02:29.371][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:29.372][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-29 16:02:29.373][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-29 16:02:29.374][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-29 16:02:29.375][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-29 16:02:29.376][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-29 16:02:29.377][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:29.378][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-06-29 16:02:29.379][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-29 16:02:29.380][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:02:29.381][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:29.382][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-29 16:02:29.382][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-29 16:02:29.382][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-29 16:02:29.382][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-29 16:02:29.382][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-29 16:02:29.383][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-29 16:02:29.384][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-29 16:02:29.385][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-29 16:02:29.386][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-29 16:02:29.387][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-29 16:02:29.389][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-29 16:02:29.395][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-29 16:02:29.396][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:02:29.397][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-29 16:02:29.398][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-29 16:02:29.399][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-29 16:02:29.400][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:02:29.401][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-06-29 16:02:29.402][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-29 16:02:29.404][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-06-29 16:02:29.405][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:29.406][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-29 16:02:29.407][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:29.408][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-29 16:02:29.409][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-29 16:02:29.410][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-29 16:02:29.452][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-29 16:02:29.454][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-29 16:02:29.455][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:29.456][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-06-29 16:02:29.457][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-29 16:02:29.458][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:02:29.459][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:29.460][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-29 16:02:29.460][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-29 16:02:29.460][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-29 16:02:29.460][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-29 16:02:29.460][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-29 16:02:29.461][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-29 16:02:29.463][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-29 16:02:29.464][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-29 16:02:29.465][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-29 16:02:29.466][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-29 16:02:29.467][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-29 16:02:29.468][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-29 16:02:29.469][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:02:29.470][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-29 16:02:29.471][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-29 16:02:29.472][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-29 16:02:29.473][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:02:29.474][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-06-29 16:02:29.476][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:29.477][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-06-29 16:02:29.478][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:29.479][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-29 16:02:29.480][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:29.481][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-29 16:02:29.482][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-29 16:02:29.483][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-29 16:02:29.484][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-29 16:02:29.485][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-29 16:02:29.486][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-29 16:02:29.487][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-06-29 16:02:29.488][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-29 16:02:29.489][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:02:29.490][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:29.491][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:02:29.492][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-29 16:02:29.493][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-29 16:02:29.494][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-29 16:02:29.495][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-29 16:02:29.496][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-29 16:02:29.497][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-29 16:02:29.499][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-29 16:02:29.501][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:02:29.502][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-29 16:02:29.504][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-29 16:02:29.505][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-29 16:02:29.506][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:02:29.507][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-06-29 16:02:29.509][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:29.511][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-06-29 16:02:29.512][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:29.513][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-29 16:02:29.514][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:29.515][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-29 16:02:29.516][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-29 16:02:29.517][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-29 16:02:29.518][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-29 16:02:29.519][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-29 16:02:29.520][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-29 16:02:29.522][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-06-29 16:02:29.523][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-29 16:02:29.525][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:02:29.526][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:29.527][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:02:29.528][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-29 16:02:29.529][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-29 16:02:29.530][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-29 16:02:29.531][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-29 16:02:29.532][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-29 16:02:29.533][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-29 16:02:29.534][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-29 16:02:29.536][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:02:29.538][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-29 16:02:29.539][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-29 16:02:29.541][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-29 16:02:29.542][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:02:29.546][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-29 16:02:29.547][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:29.548][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:29.549][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:29.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:29.553][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:29.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:29.555][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:29.556][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:29.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:29.558][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:29.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:29.560][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:29.561][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:29.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:29.563][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:29.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:29.565][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:29.566][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:29.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:29.567][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:29.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:29.569][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:29.570][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:29.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:29.572][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:29.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:29.574][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:29.575][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:29.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:29.577][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:29.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:29.579][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:29.580][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:29.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:29.582][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:29.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:29.584][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:29.585][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:29.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:29.587][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:29.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:29.589][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[2024-06-29 16:02:29.590][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:29.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:29.592][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:29.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:29.594][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:29.595][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:29.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:29.597][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:29.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:29.598][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[2024-06-29 16:02:29.599][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:29.600][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:29.601][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:29.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:29.604][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:29.605][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:29.606][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:29.607][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:29.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:29.609][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:29.610][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:29.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:29.613][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:29.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:29.615][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[2024-06-29 16:02:29.616][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:29.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:29.618][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:29.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:29.620][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:29.621][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:29.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:29.623][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:29.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:29.625][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:29.626][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:29.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:29.628][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:29.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:29.630][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[2024-06-29 16:02:29.631][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:29.632][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:29.634][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:29.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:29.636][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:29.643][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-06-29 16:02:29.649][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-06-29 16:02:29.651][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-06-29 16:02:29.652][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-06-29 16:02:29.654][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-29 16:02:29.657][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-29 16:02:29.658][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-06-29 16:02:29.660][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-06-29 16:02:29.661][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-29 16:02:29.662][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-29 16:02:29.664][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-29 16:02:29.665][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-06-29 16:02:29.667][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-06-29 16:02:29.668][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-06-29 16:02:29.669][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-06-29 16:02:29.672][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-29 16:02:29.674][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-06-29 16:02:29.675][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-06-29 16:02:29.677][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-29 16:02:29.679][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-06-29 16:02:29.681][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-06-29 16:02:29.682][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-06-29 16:02:29.684][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-06-29 16:02:29.685][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-06-29 16:02:29.687][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-06-29 16:02:29.688][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-06-29 16:02:29.689][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-06-29 16:02:29.691][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-06-29 16:02:29.692][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-06-29 16:02:29.694][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-06-29 16:02:29.695][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-06-29 16:02:29.696][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-06-29 16:02:29.698][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-06-29 16:02:29.699][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-06-29 16:02:29.700][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-06-29 16:02:29.702][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-06-29 16:02:29.703][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-06-29 16:02:29.705][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-06-29 16:02:29.706][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-06-29 16:02:29.707][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-06-29 16:02:29.709][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-06-29 16:02:29.710][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-06-29 16:02:29.711][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-06-29 16:02:29.713][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-06-29 16:02:29.714][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-06-29 16:02:29.716][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-06-29 16:02:29.717][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-06-29 16:02:29.718][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-06-29 16:02:29.720][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-06-29 16:02:29.721][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-06-29 16:02:29.723][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-06-29 16:02:29.724][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-06-29 16:02:29.725][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-06-29 16:02:29.727][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-06-29 16:02:29.728][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-06-29 16:02:29.729][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-06-29 16:02:29.731][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-06-29 16:02:29.732][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-06-29 16:02:29.733][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-06-29 16:02:29.735][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-06-29 16:02:29.736][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-06-29 16:02:29.737][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-06-29 16:02:29.739][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-06-29 16:02:29.740][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-06-29 16:02:29.742][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-06-29 16:02:29.743][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-06-29 16:02:29.745][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-29 16:02:29.746][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-29 16:02:29.747][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-06-29 16:02:29.749][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-06-29 16:02:29.750][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-06-29 16:02:29.751][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-06-29 16:02:29.753][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-06-29 16:02:29.754][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-06-29 16:02:29.755][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-06-29 16:02:29.757][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-06-29 16:02:29.758][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-06-29 16:02:29.760][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-06-29 16:02:29.761][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-06-29 16:02:29.762][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-06-29 16:02:29.764][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-06-29 16:02:29.765][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-06-29 16:02:29.766][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-06-29 16:02:29.784][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-06-29 16:02:29.786][initialize] This is biodb version 1.13.0.
biodb.DEBUG[2024-06-29 16:02:29.789][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-29 16:02:29.790][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:29.791][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:29.792][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:29.793][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:29.796][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:29.797][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:29.798][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:29.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:29.800][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:29.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:29.802][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:29.803][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:29.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:29.805][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:29.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:29.807][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:29.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:29.809][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:29.810][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:29.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:29.811][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:29.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:29.813][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:29.814][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:29.815][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:29.816][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:29.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:29.818][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:29.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:29.820][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:29.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:29.822][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:29.823][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:29.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:29.824][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:29.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:29.826][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:29.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:29.828][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:29.829][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:29.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:29.837][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:29.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:29.839][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:29.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:29.841][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:29.842][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:29.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:29.844][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:29.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:29.845][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:29.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:29.847][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:29.848][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:29.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:29.850][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:29.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:29.852][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:29.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:29.854][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:29.855][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:29.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:29.857][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:29.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:29.858][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:29.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:29.860][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:29.861][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:29.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:29.863][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:29.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:29.865][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:29.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:29.867][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:29.868][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:29.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:29.870][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:29.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:29.872][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:29.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:29.874][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:29.875][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:29.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:29.877][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:29.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:29.879][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:29.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:29.881][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:29.882][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:29.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:29.883][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:29.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:29.885][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:29.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:29.887][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:29.888][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:29.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:29.890][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:29.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:29.892][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:29.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:29.893][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:29.894][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:29.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:29.896][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:29.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:29.898][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:29.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:29.900][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:29.901][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:29.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:29.903][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:29.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:29.905][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:29.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:29.906][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:29.907][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:29.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:29.909][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:29.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:29.911][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:29.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:29.913][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:29.916][biodb$loadDefinitions] Load definitions from file "C:/Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/definitions.yml".
biodb.DEBUG[2024-06-29 16:02:29.924][self$getDbsInfo()$define] Define connector expasy.enzyme.
biodb.DEBUG[2024-06-29 16:02:29.926][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-29 16:02:29.927][self$setPropertyValue] Setting property "description" to "Write here the description of this database.".
biodb.DEBUG[2024-06-29 16:02:29.928][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:29.929][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-29 16:02:29.930][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:29.931][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-29 16:02:29.932][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:29.933][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-29 16:02:29.934][self$setPropertyValue] Setting property "entry.content.type" to "txt".
biodb.DEBUG[2024-06-29 16:02:29.935][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-29 16:02:29.936][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:29.937][self$setPropertyValue] Setting property "name" to "Expasy ENZYME database.".
biodb.DEBUG[2024-06-29 16:02:29.938][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-29 16:02:29.939][self$setPropertyValue] Setting property "parsing.expr" to "^ID\s+([0-9.]+)$".
biodb.DEBUG[2024-06-29 16:02:29.939][self$setPropertyValue] Setting property "parsing.expr" to "^CA\s+(.+?)\.?$".
biodb.DEBUG[2024-06-29 16:02:29.939][self$setPropertyValue] Setting property "parsing.expr" to "^CF\s+(.+?)\.?$".
biodb.DEBUG[2024-06-29 16:02:29.939][self$setPropertyValue] Setting property "parsing.expr" to "^DE\s+(.+?)\.?$".
biodb.DEBUG[2024-06-29 16:02:29.941][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-06-29 16:02:29.943][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-29 16:02:29.944][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-06-29 16:02:29.946][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-29 16:02:29.947][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-29 16:02:29.948][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-29 16:02:29.949][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-29 16:02:29.950][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-29 16:02:29.951][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-29 16:02:29.952][self$setPropertyValue] Setting property "urls" to "https://enzyme.expasy.org/".
biodb.DEBUG[2024-06-29 16:02:29.953][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-29 16:02:29.954][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-29 16:02:29.955][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:29.956][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:02:29.962][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-29 16:02:29.981][super$initialize] Initialize connector expasy.enzyme.
biodb.DEBUG[2024-06-29 16:02:29.982][super$initialize] Register connector expasy.enzyme with the request scheduler
biodb.DEBUG[2024-06-29 16:02:29.985][private$bdb$getRequestScheduler()$re ...] Register connector expasy.enzyme.
biodb.DEBUG[2024-06-29 16:02:29.989][private$addConnectorRules] Create new rule for URL "enzyme.expasy.org" of connector "expasy.enzyme".
biodb.DEBUG[2024-06-29 16:02:29.992][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-29 16:02:29.993][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-29 16:02:29.994][biodb$getFactory()$createConn] Creating new connector expasy.enzyme for database class expasy.enzyme .
biodb.INFO [2024-06-29 16:02:30.003][biodb::testThat]
biodb.INFO [2024-06-29 16:02:30.004][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-06-29 16:02:30.005][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-29 16:02:30.006][biodb::testThat]
biodb.TRACE[2024-06-29 16:02:30.010][loadFileContents] Loaded 1 files from cache: [1]: "C:/Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/testref/entry-expasy.enzyme-1.1.1.1-content.txt".
biodb.DEBUG[2024-06-29 16:02:30.012][biodb$getFactory()$createEntryFromCo ...] Creating Expasy ENZYME database. entries from 1 content(s).
biodb.DEBUG[2024-06-29 16:02:30.014][biodb$getFactory()$createEntryFromCo ...] Parsing 1 Expasy ENZYME database. entries.
biodb.DEBUG[2024-06-29 16:02:30.028][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-29 16:02:30.029][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:30.030][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:30.043][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:30.044][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:30.045][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:30.046][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.TRACE[2024-06-29 16:02:30.055][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:30.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:30.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.080][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-29 16:02:30.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-29 16:02:30.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.094][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-29 16:02:30.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-29 16:02:30.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.098][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:02:30.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:02:30.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.106][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-06-29 16:02:30.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-29 16:02:30.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.110][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-29 16:02:30.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-29 16:02:30.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.115][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-29 16:02:30.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-29 16:02:30.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.120][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-29 16:02:30.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-29 16:02:30.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.124][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-06-29 16:02:30.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-29 16:02:30.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.142][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:02:30.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:02:30.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.146][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:02:30.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:02:30.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.217][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:02:30.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:02:30.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.221][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:02:30.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:02:30.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.226][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:02:30.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:02:30.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.230][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:02:30.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:02:30.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.234][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:02:30.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:02:30.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.239][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:30.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:30.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.243][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:02:30.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:02:30.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.247][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:30.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:30.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.251][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:30.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:30.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.257][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:30.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:30.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.261][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:30.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:30.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.266][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:30.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:30.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.270][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:30.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:30.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-29 16:02:30.274][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 1.1.1.1.
biodb.TRACE[2024-06-29 16:02:30.277][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-29 16:02:30.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-29 16:02:30.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.281][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-29 16:02:30.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-29 16:02:30.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.285][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-29 16:02:30.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-29 16:02:30.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.290][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-29 16:02:30.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-29 16:02:30.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.319][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:30.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:30.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.344][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:02:30.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:02:30.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.354][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:30.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:30.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.364][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:30.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:30.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.368][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:30.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:30.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.374][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:30.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:30.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.378][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:30.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:30.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.382][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:30.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:30.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.387][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:02:30.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:02:30.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.391][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:02:30.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:02:30.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.395][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:02:30.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:02:30.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.407][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:30.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:30.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.412][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:30.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:30.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.416][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:30.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:30.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.420][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:30.421][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:30.422][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.423][ef$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.424][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:30.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:30.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.437][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:02:30.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:02:30.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.441][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:02:30.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:02:30.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.445][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:02:30.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:02:30.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.449][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:02:30.450][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:02:30.451][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.453][ef$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.454][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:02:30.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:02:30.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.466][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-29 16:02:30.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-29 16:02:30.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.470][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-29 16:02:30.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-29 16:02:30.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.474][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-29 16:02:30.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-29 16:02:30.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.479][ef$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-29 16:02:30.480][ef$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-29 16:02:30.481][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.482][ef$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.483][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-29 16:02:30.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-29 16:02:30.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.495][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-29 16:02:30.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-29 16:02:30.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.500][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-29 16:02:30.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-29 16:02:30.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.504][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-29 16:02:30.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-29 16:02:30.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.508][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-29 16:02:30.509][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-29 16:02:30.510][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.511][ef$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.512][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-29 16:02:30.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-29 16:02:30.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.529][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:30.530][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:30.532][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.532][ef$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.538][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-29 16:02:30.539][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-29 16:02:30.540][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.541][ef$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.547][ef$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-29 16:02:30.548][ef$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-29 16:02:30.549][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.550][ef$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.556][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:02:30.557][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:02:30.558][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.559][ef$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.575][loadFileContents] Loaded 1 files from cache: [1]: "C:/Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/testref/entry-expasy.enzyme-1.1.1.54-content.txt".
biodb.DEBUG[2024-06-29 16:02:30.604][biodb$getFactory()$createEntryFromCo ...] Creating Expasy ENZYME database. entries from 1 content(s).
biodb.DEBUG[2024-06-29 16:02:30.606][biodb$getFactory()$createEntryFromCo ...] Parsing 1 Expasy ENZYME database. entries.
biodb.DEBUG[2024-06-29 16:02:30.608][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-29 16:02:30.609][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:30.610][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:30.617][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:30.618][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:30.620][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:30.621][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.TRACE[2024-06-29 16:02:30.625][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:30.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:30.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.630][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-29 16:02:30.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-29 16:02:30.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.635][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:02:30.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:02:30.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.640][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-06-29 16:02:30.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-29 16:02:30.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.644][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:02:30.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:02:30.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.649][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:02:30.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:02:30.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.653][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:30.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:30.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.665][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:02:30.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:02:30.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.669][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:30.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:30.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.677][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:30.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:30.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.683][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:30.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:30.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.688][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:30.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:30.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.692][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:30.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:30.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.699][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:30.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:30.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-29 16:02:30.704][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 1.1.1.54.
biodb.TRACE[2024-06-29 16:02:30.726][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-29 16:02:30.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-29 16:02:30.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.731][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-29 16:02:30.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-29 16:02:30.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.736][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-29 16:02:30.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-29 16:02:30.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.740][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-29 16:02:30.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-29 16:02:30.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.748][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:30.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:30.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.760][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:02:30.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:02:30.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.771][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:30.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:30.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.778][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:30.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:30.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.783][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:30.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:30.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.789][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:30.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:30.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.794][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:30.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:30.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.798][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:30.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:30.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.805][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:02:30.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:02:30.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.809][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:02:30.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:02:30.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.813][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:02:30.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:02:30.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.839][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:30.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:30.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.844][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:30.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:30.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.848][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:30.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:30.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.853][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:30.854][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:30.855][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.856][ef$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.857][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:30.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:30.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.872][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:02:30.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:02:30.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.877][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:02:30.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:02:30.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.881][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:02:30.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:02:30.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.885][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:02:30.886][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:02:30.887][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.888][ef$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.889][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:02:30.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:02:30.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.902][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-29 16:02:30.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-29 16:02:30.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.907][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-29 16:02:30.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-29 16:02:30.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.911][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-29 16:02:30.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-29 16:02:30.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.915][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-29 16:02:30.916][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-29 16:02:30.917][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.918][ef$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.919][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-29 16:02:30.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-29 16:02:30.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.932][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:30.933][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:30.934][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.935][ef$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.941][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-29 16:02:30.942][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-29 16:02:30.944][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.945][ef$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:30.951][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:02:30.952][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:02:30.953][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:30.954][ef$get] fields variable is a list.
biodb.INFO [2024-06-29 16:02:30.967][biodb::testThat]
biodb.INFO [2024-06-29 16:02:30.968][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-06-29 16:02:30.969][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-29 16:02:30.971][biodb::testThat]
biodb.DEBUG[2024-06-29 16:02:30.974][private$loadEntries] Creating entries from ids [2]: "1.1.1.1, 1.1.1.54".
biodb.DEBUG[2024-06-29 16:02:30.980][conn$getEntryContent] Get Expasy ENZYME database. entry content(s) for 2 id(s)...
biodb.TRACE[2024-06-29 16:02:30.986][cch$loadFileContent] Trying to load 2 files from cache: [2]: "1.1.1.1, 1.1.1.54".
biodb.INFO [2024-06-29 16:02:30.988][self$getFolderPath] Create cache folder "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280" for "expasy.enzyme-b59b84d962b6741050ba8f70ff4db280".
biodb.TRACE[2024-06-29 16:02:30.989][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2024-06-29 16:02:30.991][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-29 16:02:30.992][conn$getEntryContent] 0 Expasy ENZYME database. entry content(s) loaded from cache.
biodb.DEBUG[2024-06-29 16:02:30.993][conn$getEntryContent] 2 entry content(s) need to be fetched from Expasy ENZYME database. database "https://enzyme.expasy.org/".
biodb.DEBUG[2024-06-29 16:02:30.994][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-29 16:02:30.995][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-29 16:02:31.000][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-29 16:02:31.001][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:31.010][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:31.017][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:31.018][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:31.020][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:31.021][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:31.023][scheduler$sendRequest] Getting content of get URL request "https://enzyme.expasy.org/EC/1.1.1.1.txt".
biodb.DEBUG[2024-06-29 16:02:31.045][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-29 16:02:31.046][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-29 16:02:31.047][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/EC/1.1.1.1.txt".
biodb.TRACE[2024-06-29 16:02:31.801][doesRCurlRequestUrlExist] According to RCurl, URL https://enzyme.expasy.org/EC/1.1.1.1.txt does not exist.
biodb.TRACE[2024-06-29 16:02:31.803][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-29 16:02:31.804][getUrlRequestResult] URL "https://enzyme.expasy.org/EC/1.1.1.1.txt" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-29 16:02:31.805][getBaseUrlRequestResult] Using base::url() for sending request (https://enzyme.expasy.org/EC/1.1.1.1.txt).
biodb.DEBUG[2024-06-29 16:02:32.234][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-29 16:02:32.237][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a52675cfd2f0c2b41556caa64d9341e3.content"
biodb.TRACE[2024-06-29 16:02:32.252][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a52675cfd2f0c2b41556caa64d9341e3.request"
biodb.DEBUG[2024-06-29 16:02:32.256][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-29 16:02:32.258][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:32.259][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:32.267][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:32.268][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:32.269][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:32.270][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:32.288][scheduler$sendRequest] Getting content of get URL request "https://enzyme.expasy.org/EC/1.1.1.54.txt".
biodb.DEBUG[2024-06-29 16:02:32.303][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-29 16:02:32.305][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-29 16:02:32.324][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/EC/1.1.1.54.txt".
biodb.TRACE[2024-06-29 16:02:32.548][doesRCurlRequestUrlExist] According to RCurl, URL https://enzyme.expasy.org/EC/1.1.1.54.txt does not exist.
biodb.TRACE[2024-06-29 16:02:32.550][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-29 16:02:32.551][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[2024-06-29 16:02:32.552][getBaseUrlRequestResult] Using base::url() for sending request (https://enzyme.expasy.org/EC/1.1.1.54.txt).
biodb.DEBUG[2024-06-29 16:02:32.984][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-29 16:02:32.987][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a9b93566a091cbe35a06e4b3871f95c9.content"
biodb.TRACE[2024-06-29 16:02:32.991][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a9b93566a091cbe35a06e4b3871f95c9.request"
biodb.TRACE[2024-06-29 16:02:32.994][private$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[2024-06-29 16:02:32.996][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-29 16:02:32.998][self$createEntryFromContent] Creating Expasy ENZYME database. entries from 2 content(s).
biodb.DEBUG[2024-06-29 16:02:32.999][self$createEntryFromContent] Parsing 2 Expasy ENZYME database. entries.
biodb.DEBUG[2024-06-29 16:02:33.001][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-29 16:02:33.002][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:33.003][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:33.009][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:33.010][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:33.011][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:33.012][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-29 16:02:33.016][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:33.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:33.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:33.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:33.021][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-29 16:02:33.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-29 16:02:33.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:33.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:33.026][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:02:33.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:02:33.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:33.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:33.030][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-06-29 16:02:33.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-29 16:02:33.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:33.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:33.034][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:02:33.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:02:33.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:33.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:33.039][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:02:33.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:02:33.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:33.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:33.043][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:02:33.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:02:33.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:33.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:33.047][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:02:33.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:02:33.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:33.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:33.051][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:02:33.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:02:33.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:33.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:33.057][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:02:33.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:02:33.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:33.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:33.061][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:02:33.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:02:33.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:33.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:33.066][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:33.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:33.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:33.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:33.070][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:02:33.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:02:33.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:33.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:33.074][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:33.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:33.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:33.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:33.078][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:33.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:33.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:33.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:33.083][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:33.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:33.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:33.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-29 16:02:33.096][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-29 16:02:33.097][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:33.098][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:33.105][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:33.106][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:33.107][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:33.108][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-29 16:02:33.110][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:33.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:33.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:33.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:33.115][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-29 16:02:33.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-29 16:02:33.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:33.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:33.120][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:02:33.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:02:33.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:33.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:33.124][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-06-29 16:02:33.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-29 16:02:33.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:33.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:33.129][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:02:33.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:02:33.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:33.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:33.133][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:02:33.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:02:33.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:33.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:33.138][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:33.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:33.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:33.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:33.142][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:02:33.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-29 16:02:33.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:33.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:33.147][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:33.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:33.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:33.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:33.151][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:33.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:33.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:33.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:33.156][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:33.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:33.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:33.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:33.161][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:33.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:33.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:33.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:33.166][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:33.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:33.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:33.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:33.171][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:33.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:33.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:33.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:33.176][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:33.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:33.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:33.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:33.181][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:33.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:33.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:33.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:33.185][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:33.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:33.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:33.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-29 16:02:33.190][self$createEntryFromContent] Accession numbers: 1.1.1.1, 1.1.1.54.
biodb.TRACE[2024-06-29 16:02:33.191][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-06-29 16:02:33.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-06-29 16:02:33.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:33.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:33.196][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-06-29 16:02:33.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-06-29 16:02:33.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:33.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:33.200][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-06-29 16:02:33.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-06-29 16:02:33.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:33.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:33.210][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-06-29 16:02:33.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-06-29 16:02:33.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:33.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:33.215][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-06-29 16:02:33.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-06-29 16:02:33.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:33.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:33.224][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-06-29 16:02:33.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-06-29 16:02:33.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:33.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-29 16:02:33.237][biodb::testThat]
biodb.INFO [2024-06-29 16:02:33.238][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-06-29 16:02:33.239][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-29 16:02:33.240][biodb::testThat]
biodb.TRACE[2024-06-29 16:02:33.243][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:02:33.245][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:02:33.247][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:33.250][ef$get] fields variable is a list.
biodb.DEBUG[2024-06-29 16:02:33.252][function(conn, opt)] Testing searchForEntries() with entry "1.1.1.1" and field "name".
biodb.TRACE[2024-06-29 16:02:33.289][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:02:33.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:02:33.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:33.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:33.294][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:02:33.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:02:33.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:33.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:33.301][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:02:33.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:02:33.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:33.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-29 16:02:33.309][function(conn, opt)] With value "alcohol dehydrogenase".
biodb.DEBUG[2024-06-29 16:02:33.311][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://enzyme.expasy.org/enzyme-byname.html?alcohol dehydrogenase".
biodb.DEBUG[2024-06-29 16:02:33.315][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-29 16:02:33.316][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-29 16:02:33.317][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase".
biodb.TRACE[2024-06-29 16:02:33.540][doesRCurlRequestUrlExist] According to RCurl, URL https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase does not exist.
biodb.TRACE[2024-06-29 16:02:33.542][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-29 16:02:33.543][getUrlRequestResult] URL "https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-29 16:02:33.545][getBaseUrlRequestResult] Using base::url() for sending request (https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase).
biodb.DEBUG[2024-06-29 16:02:33.995][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-29 16:02:33.998][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.content"
biodb.TRACE[2024-06-29 16:02:34.002][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.request"
biodb.DEBUG[2024-06-29 16:02:34.010][function(conn, opt)] With found IDs [1]: "1.1.1.1".
biodb.INFO [2024-06-29 16:02:34.036][biodb::testThat]
biodb.INFO [2024-06-29 16:02:34.038][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-06-29 16:02:34.039][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-29 16:02:34.040][biodb::testThat]
biodb.TRACE[2024-06-29 16:02:34.080][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:02:34.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:02:34.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:34.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:34.085][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:02:34.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:02:34.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:34.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:34.089][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:02:34.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:02:34.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:34.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-29 16:02:34.118][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://enzyme.expasy.org/enzyme-byname.html?alcohol dehydrogenase".
biodb.DEBUG[2024-06-29 16:02:34.121][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-29 16:02:34.134][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f603fa2a57aec59588edc37541c6f6d5".
biodb.TRACE[2024-06-29 16:02:34.136][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-29 16:02:34.141][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.content".
biodb.INFO [2024-06-29 16:02:34.176][biodb::testThat]
biodb.INFO [2024-06-29 16:02:34.178][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-06-29 16:02:34.179][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-29 16:02:34.180][biodb::testThat]
biodb.TRACE[2024-06-29 16:02:34.194][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-29 16:02:34.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-29 16:02:34.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:34.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:34.201][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-29 16:02:34.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-29 16:02:34.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:34.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:34.206][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-29 16:02:34.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-29 16:02:34.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:34.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:34.213][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-29 16:02:34.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-29 16:02:34.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:34.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:34.251][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-29 16:02:34.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-29 16:02:34.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:34.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:34.256][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-29 16:02:34.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-29 16:02:34.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:34.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:34.261][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-29 16:02:34.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-29 16:02:34.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:34.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:34.267][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-29 16:02:34.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-29 16:02:34.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:34.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-29 16:02:34.280][biodb::testThat]
biodb.INFO [2024-06-29 16:02:34.281][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-06-29 16:02:34.283][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-29 16:02:34.284][biodb::testThat]
biodb.INFO [2024-06-29 16:02:34.301][biodb::testThat]
biodb.INFO [2024-06-29 16:02:34.302][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-06-29 16:02:34.303][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-29 16:02:34.304][biodb::testThat]
biodb.INFO [2024-06-29 16:02:34.314][biodb::testThat]
biodb.INFO [2024-06-29 16:02:34.315][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-06-29 16:02:34.316][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-29 16:02:34.317][biodb::testThat]
biodb.DEBUG[2024-06-29 16:02:34.329][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[2024-06-29 16:02:34.553][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 [2024-06-29 16:02:35.136][biodb::testThat]
biodb.INFO [2024-06-29 16:02:35.138][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-06-29 16:02:35.139][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-29 16:02:35.140][biodb::testThat]
biodb.DEBUG[2024-06-29 16:02:35.381][getUrlContent] Use base::url() for downloading content of URL https://enzyme.expasy.org/images/1.1.1.1/image.png.
biodb.TRACE[2024-06-29 16:02:35.945][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:02:35.947][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:02:35.948][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:35.949][ef$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:35.950][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:02:35.952][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:02:35.954][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:35.955][ef$get] fields variable is a list.
biodb.INFO [2024-06-29 16:02:35.956][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-06-29 16:02:35.958][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector expasy.enzyme from the request scheduler
biodb.INFO [2024-06-29 16:02:35.959][self$deleteConn] Connector "expasy.enzyme" deleted.
biodb.DEBUG[2024-06-29 16:02:35.960][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-06-29 16:02:35.961][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:35.962][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:35.963][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:35.964][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:35.965][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:35.966][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-06-29 16:02:35.976][biodb::testContext]
biodb.INFO [2024-06-29 16:02:35.977][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-29 16:02:35.978][biodb::testContext] Test context - Example long tests
biodb.INFO [2024-06-29 16:02:35.979][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-29 16:02:35.980][biodb::testContext]
biodb.INFO [2024-06-29 16:02:35.983][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.13.0.
biodb.DEBUG[2024-06-29 16:02:35.992][self$loadDefinitions] Load definitions from file "C:/Users/biocbuild/bbs-3.20-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2024-06-29 16:02:35.996][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-29 16:02:35.997][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-06-29 16:02:35.999][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-06-29 16:02:36.000][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:36.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:36.001][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:36.003][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-06-29 16:02:36.004][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-06-29 16:02:36.005][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:36.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:36.006][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:36.007][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-06-29 16:02:36.008][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-06-29 16:02:36.009][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:36.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:36.011][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:36.012][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-06-29 16:02:36.013][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-06-29 16:02:36.014][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-06-29 16:02:36.015][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:36.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:36.017][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:36.018][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-06-29 16:02:36.019][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-06-29 16:02:36.020][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-06-29 16:02:36.021][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:36.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:36.023][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:36.024][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-06-29 16:02:36.026][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-06-29 16:02:36.026][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:36.027][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:36.028][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:36.029][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-06-29 16:02:36.030][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-06-29 16:02:36.031][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-06-29 16:02:36.032][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:36.033][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:36.034][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:36.035][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-06-29 16:02:36.036][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-06-29 16:02:36.037][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:36.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:36.039][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:36.040][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-06-29 16:02:36.041][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-06-29 16:02:36.042][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-06-29 16:02:36.043][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:36.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:36.045][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:36.047][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-06-29 16:02:36.048][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-06-29 16:02:36.049][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-06-29 16:02:36.050][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-06-29 16:02:36.051][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-06-29 16:02:36.052][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-06-29 16:02:36.053][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:36.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:36.055][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:36.056][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-06-29 16:02:36.057][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-06-29 16:02:36.058][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:36.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:36.061][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:36.062][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-06-29 16:02:36.063][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-06-29 16:02:36.064][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:36.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:36.066][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:36.067][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-06-29 16:02:36.068][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-06-29 16:02:36.069][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:36.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:36.071][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:36.072][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-06-29 16:02:36.073][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-06-29 16:02:36.074][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:36.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:36.076][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:36.077][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-06-29 16:02:36.078][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-06-29 16:02:36.079][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:36.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:36.080][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:36.081][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-06-29 16:02:36.082][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-06-29 16:02:36.087][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-06-29 16:02:36.088][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:36.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:36.090][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:36.091][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-06-29 16:02:36.092][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-06-29 16:02:36.093][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-06-29 16:02:36.095][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:36.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:36.097][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[2024-06-29 16:02:36.099][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-06-29 16:02:36.101][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-29 16:02:36.108][self$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[2024-06-29 16:02:36.109][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:36.110][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-29 16:02:36.112][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:36.113][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-29 16:02:36.115][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-29 16:02:36.116][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-29 16:02:36.118][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-29 16:02:36.119][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-29 16:02:36.120][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:36.122][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-06-29 16:02:36.123][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-29 16:02:36.124][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:02:36.126][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:36.128][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-29 16:02:36.128][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-29 16:02:36.128][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-29 16:02:36.128][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-29 16:02:36.128][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-29 16:02:36.130][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-29 16:02:36.140][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-29 16:02:36.142][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-29 16:02:36.143][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-29 16:02:36.144][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-29 16:02:36.146][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-29 16:02:36.147][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-29 16:02:36.148][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:02:36.150][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-29 16:02:36.151][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-29 16:02:36.153][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-29 16:02:36.155][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:02:36.156][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-06-29 16:02:36.158][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-29 16:02:36.160][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-06-29 16:02:36.161][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:36.162][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-29 16:02:36.163][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:36.164][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-29 16:02:36.166][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-29 16:02:36.167][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-29 16:02:36.168][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-29 16:02:36.169][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-29 16:02:36.171][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:36.172][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-06-29 16:02:36.174][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-29 16:02:36.175][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:02:36.176][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:36.178][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-29 16:02:36.178][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-29 16:02:36.178][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-29 16:02:36.178][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-29 16:02:36.178][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-29 16:02:36.179][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-29 16:02:36.180][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-29 16:02:36.181][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-29 16:02:36.182][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-29 16:02:36.184][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-29 16:02:36.185][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-29 16:02:36.186][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-29 16:02:36.187][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:02:36.188][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-29 16:02:36.189][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-29 16:02:36.190][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-29 16:02:36.192][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:02:36.193][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-06-29 16:02:36.195][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:36.196][self$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[2024-06-29 16:02:36.197][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:36.198][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-29 16:02:36.200][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:36.201][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-29 16:02:36.202][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-29 16:02:36.203][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-29 16:02:36.204][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-29 16:02:36.206][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-29 16:02:36.207][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-29 16:02:36.208][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-06-29 16:02:36.209][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-29 16:02:36.210][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:02:36.211][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:36.213][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:02:36.214][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-29 16:02:36.215][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-29 16:02:36.216][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-29 16:02:36.217][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-29 16:02:36.218][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-29 16:02:36.219][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-29 16:02:36.220][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-29 16:02:36.221][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:02:36.223][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-29 16:02:36.224][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-29 16:02:36.225][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-29 16:02:36.226][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:02:36.227][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-06-29 16:02:36.229][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:36.230][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-06-29 16:02:36.231][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:36.233][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-29 16:02:36.234][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:36.235][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-29 16:02:36.236][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-29 16:02:36.237][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-29 16:02:36.238][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-29 16:02:36.239][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-29 16:02:36.246][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-29 16:02:36.247][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-06-29 16:02:36.249][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-29 16:02:36.250][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:02:36.254][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:36.255][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:02:36.256][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-29 16:02:36.257][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-29 16:02:36.258][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-29 16:02:36.260][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-29 16:02:36.262][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-29 16:02:36.264][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-29 16:02:36.265][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-29 16:02:36.267][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:02:36.268][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-29 16:02:36.270][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-29 16:02:36.272][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-29 16:02:36.273][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:02:36.275][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-29 16:02:36.276][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:36.277][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:36.278][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:36.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:36.281][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:36.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:36.284][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:36.286][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:36.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:36.289][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:36.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:36.291][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:36.292][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:36.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:36.295][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:36.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:36.297][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:36.298][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:36.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:36.300][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:36.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:36.302][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:36.304][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:36.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:36.306][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:36.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:36.308][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:36.309][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:36.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:36.311][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:36.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:36.313][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:36.314][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:36.316][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:36.317][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:36.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:36.319][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:36.320][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:36.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:36.322][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:36.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:36.325][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:36.327][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:36.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:36.329][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:36.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:36.331][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:36.332][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:36.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:36.334][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:36.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:36.336][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:36.337][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:36.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:36.339][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:36.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:36.341][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:36.342][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:36.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:36.344][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:36.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:36.347][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:36.348][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:36.349][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:36.351][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:36.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:36.353][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:36.355][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:36.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:36.358][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:36.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:36.361][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:36.362][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:36.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:36.365][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:36.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:36.367][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:36.368][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:36.369][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:36.371][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:36.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:36.374][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:36.375][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:36.376][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:36.377][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:36.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:36.385][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:36.386][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-06-29 16:02:36.387][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-06-29 16:02:36.389][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-06-29 16:02:36.390][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-06-29 16:02:36.392][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-29 16:02:36.393][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-29 16:02:36.395][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-06-29 16:02:36.396][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-06-29 16:02:36.398][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-29 16:02:36.399][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-29 16:02:36.401][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-29 16:02:36.402][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-06-29 16:02:36.403][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-06-29 16:02:36.405][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-06-29 16:02:36.406][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-06-29 16:02:36.408][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-29 16:02:36.409][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-06-29 16:02:36.411][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-06-29 16:02:36.412][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-29 16:02:36.414][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-06-29 16:02:36.415][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-06-29 16:02:36.417][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-06-29 16:02:36.418][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-06-29 16:02:36.420][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-06-29 16:02:36.421][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-06-29 16:02:36.423][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-06-29 16:02:36.424][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-06-29 16:02:36.426][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-06-29 16:02:36.428][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-06-29 16:02:36.430][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-06-29 16:02:36.432][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-06-29 16:02:36.434][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-06-29 16:02:36.436][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-06-29 16:02:36.438][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-06-29 16:02:36.441][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-06-29 16:02:36.442][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-06-29 16:02:36.444][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-06-29 16:02:36.446][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-06-29 16:02:36.447][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-06-29 16:02:36.449][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-06-29 16:02:36.450][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-06-29 16:02:36.452][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-06-29 16:02:36.453][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-06-29 16:02:36.455][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-06-29 16:02:36.456][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-06-29 16:02:36.458][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-06-29 16:02:36.459][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-06-29 16:02:36.461][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-06-29 16:02:36.462][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-06-29 16:02:36.464][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-06-29 16:02:36.465][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-06-29 16:02:36.466][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-06-29 16:02:36.468][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-06-29 16:02:36.469][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-06-29 16:02:36.472][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-06-29 16:02:36.473][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-06-29 16:02:36.475][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-06-29 16:02:36.477][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-06-29 16:02:36.478][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-06-29 16:02:36.480][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-06-29 16:02:36.482][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-06-29 16:02:36.484][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-06-29 16:02:36.486][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-06-29 16:02:36.488][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-06-29 16:02:36.490][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-06-29 16:02:36.492][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-06-29 16:02:36.500][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-29 16:02:36.502][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-29 16:02:36.504][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-06-29 16:02:36.505][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-06-29 16:02:36.507][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-06-29 16:02:36.508][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-06-29 16:02:36.509][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-06-29 16:02:36.511][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-06-29 16:02:36.512][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-06-29 16:02:36.514][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-06-29 16:02:36.515][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-06-29 16:02:36.517][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-06-29 16:02:36.518][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-06-29 16:02:36.520][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-06-29 16:02:36.521][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-06-29 16:02:36.523][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-06-29 16:02:36.524][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-06-29 16:02:36.526][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-06-29 16:02:36.529][initialize] This is biodb version 1.13.0.
biodb.DEBUG[2024-06-29 16:02:36.530][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-29 16:02:36.531][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:36.532][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:36.533][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:36.534][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:36.535][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:36.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:36.537][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:36.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:36.539][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:36.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:36.541][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:36.542][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:36.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:36.544][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:36.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:36.546][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:36.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:36.548][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:36.549][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:36.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:36.551][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:36.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:36.553][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:36.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:36.555][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:36.556][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:36.558][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:36.559][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:36.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:36.562][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:36.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:36.565][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:36.566][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:36.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:36.569][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:36.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:36.572][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:36.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:36.574][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:36.575][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:36.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:36.577][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:36.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:36.579][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:36.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:36.581][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:36.582][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:36.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:36.584][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:36.585][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:36.586][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:36.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:36.588][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:36.589][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:36.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:36.591][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:36.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:36.593][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:36.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:36.595][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:36.596][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:36.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:36.598][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:36.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:36.601][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:36.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:36.604][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:36.605][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:36.606][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:36.607][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:36.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:36.610][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:36.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:36.612][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:36.613][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:36.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:36.621][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:36.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:36.623][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:36.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:36.626][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:36.627][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:36.628][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:36.629][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:36.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:36.631][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:36.632][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:36.633][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[2024-06-29 16:02:36.634][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:36.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:36.636][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:36.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:36.639][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:36.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:36.641][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:36.642][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:36.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:36.645][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:36.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:36.647][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:36.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:36.649][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:36.650][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:36.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:36.652][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:36.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:36.654][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:36.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:36.656][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:36.657][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:36.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:36.659][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:36.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:36.661][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:36.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:36.663][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:36.664][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:36.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:36.666][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:36.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:36.668][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:36.674][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:36.681][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:36.685][biodb$loadDefinitions] Load definitions from file "C:/Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/definitions.yml".
biodb.DEBUG[2024-06-29 16:02:36.688][self$getDbsInfo()$define] Define connector expasy.enzyme.
biodb.DEBUG[2024-06-29 16:02:36.690][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-29 16:02:36.691][self$setPropertyValue] Setting property "description" to "Write here the description of this database.".
biodb.DEBUG[2024-06-29 16:02:36.692][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:36.693][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-29 16:02:36.694][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:36.696][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-29 16:02:36.697][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:36.698][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-29 16:02:36.699][self$setPropertyValue] Setting property "entry.content.type" to "txt".
biodb.DEBUG[2024-06-29 16:02:36.700][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-29 16:02:36.701][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:36.702][self$setPropertyValue] Setting property "name" to "Expasy ENZYME database.".
biodb.DEBUG[2024-06-29 16:02:36.703][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-29 16:02:36.705][self$setPropertyValue] Setting property "parsing.expr" to "^ID\s+([0-9.]+)$".
biodb.DEBUG[2024-06-29 16:02:36.705][self$setPropertyValue] Setting property "parsing.expr" to "^CA\s+(.+?)\.?$".
biodb.DEBUG[2024-06-29 16:02:36.705][self$setPropertyValue] Setting property "parsing.expr" to "^CF\s+(.+?)\.?$".
biodb.DEBUG[2024-06-29 16:02:36.705][self$setPropertyValue] Setting property "parsing.expr" to "^DE\s+(.+?)\.?$".
biodb.DEBUG[2024-06-29 16:02:36.706][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-06-29 16:02:36.707][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-29 16:02:36.708][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-06-29 16:02:36.709][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-29 16:02:36.710][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-29 16:02:36.711][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-29 16:02:36.712][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-29 16:02:36.713][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-29 16:02:36.714][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-29 16:02:36.715][self$setPropertyValue] Setting property "urls" to "https://enzyme.expasy.org/".
biodb.DEBUG[2024-06-29 16:02:36.716][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-29 16:02:36.717][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-29 16:02:36.718][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:36.719][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:02:36.720][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-29 16:02:36.724][super$initialize] Initialize connector expasy.enzyme.
biodb.DEBUG[2024-06-29 16:02:36.725][super$initialize] Register connector expasy.enzyme with the request scheduler
biodb.DEBUG[2024-06-29 16:02:36.726][private$bdb$getRequestScheduler()$re ...] Register connector expasy.enzyme.
biodb.DEBUG[2024-06-29 16:02:36.728][private$addConnectorRules] Create new rule for URL "enzyme.expasy.org" of connector "expasy.enzyme".
biodb.DEBUG[2024-06-29 16:02:36.729][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-29 16:02:36.730][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-29 16:02:36.731][biodb$getFactory()$createConn] Creating new connector expasy.enzyme for database class expasy.enzyme .
biodb.INFO [2024-06-29 16:02:36.733][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-06-29 16:02:36.734][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector expasy.enzyme from the request scheduler
biodb.INFO [2024-06-29 16:02:36.735][self$deleteConn] Connector "expasy.enzyme" deleted.
biodb.DEBUG[2024-06-29 16:02:36.736][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-06-29 16:02:36.737][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:36.738][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:36.739][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:36.740][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:36.741][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:36.748][FUN] Functions in observer 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:
###
###   C:\Users\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 'C:/Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck'
* using R version 4.4.1 (2024-06-14 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using options '--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error'
* checking for file 'biodbExpasy/DESCRIPTION' ... OK
* this is package 'biodbExpasy' version '1.9.0'
* 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
  'C:/Users/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)