Back to Long Tests report for BioC 3.19

This page was generated on 2024-05-04 23:55:02 -0400 (Sat, 04 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4753
palomino3Windows Server 2022 Datacenterx644.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" 4486
lconwaymacOS 12.7.1 Montereyx86_644.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" 4519
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 7/33HostnameOS / ArchCHECK
biodbExpasy 1.8.0  (landing page)
Pierrick Roger
Snapshot Date: 2024-05-04 09:55:02 -0400 (Sat, 04 May 2024)
git_url: https://git.bioconductor.org/packages/biodbExpasy
git_branch: RELEASE_3_19
git_last_commit: de004e8
git_last_commit_date: 2024-04-30 11:41:12 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK  
palomino3Windows Server 2022 Datacenter / x64  OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK  

CHECK results for biodbExpasy on nebbiolo1


To the developers/maintainers of the biodbExpasy package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: biodbExpasy
Version: 1.8.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbExpasy_1.8.0.tar.gz
StartedAt: 2024-05-04 16:06:21 -0400 (Sat, 04 May 2024)
EndedAt: 2024-05-04 16:07:08 -0400 (Sat, 04 May 2024)
EllapsedTime: 46.4 seconds
RetCode: 0
Status:   OK  
CheckDir: biodbExpasy.Rcheck
Warnings: 0

Tests output

biodbExpasy.Rcheck/tests/testthat.Rout


R version 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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

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Type 'contributors()' for more information and
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Type 'demo()' for some demos, 'help()' for on-line help, or
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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 [2024-05-04 16:06:57.386][biodb::testContext]
biodb.INFO [2024-05-04 16:06:57.388][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-04 16:06:57.389][biodb::testContext] Test context - Generic long tests
biodb.INFO [2024-05-04 16:06:57.390][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-04 16:06:57.391][biodb::testContext]
biodb.INFO [2024-05-04 16:06:57.398][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-05-04 16:06:57.400][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-05-04 16:06:57.408][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-04 16:06:57.409][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-05-04 16:06:57.410][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-05-04 16:06:57.411][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:06:57.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:06:57.413][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:06:57.414][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-05-04 16:06:57.434][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-05-04 16:06:57.435][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:06:57.436][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:06:57.436][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:06:57.437][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-05-04 16:06:57.439][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-05-04 16:06:57.439][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:06:57.440][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:06:57.441][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:06:57.442][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-05-04 16:06:57.443][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-05-04 16:06:57.444][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-05-04 16:06:57.445][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:06:57.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:06:57.447][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:06:57.448][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-05-04 16:06:57.449][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-05-04 16:06:57.450][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-05-04 16:06:57.451][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:06:57.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:06:57.453][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:06:57.454][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-05-04 16:06:57.455][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-05-04 16:06:57.456][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:06:57.457][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:06:57.458][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:06:57.459][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-05-04 16:06:57.460][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-05-04 16:06:57.461][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-05-04 16:06:57.462][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:06:57.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:06:57.463][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:06:57.464][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-05-04 16:06:57.466][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-05-04 16:06:57.466][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:06:57.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:06:57.468][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:06:57.469][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-05-04 16:06:57.470][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-05-04 16:06:57.471][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-05-04 16:06:57.472][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:06:57.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:06:57.474][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:06:57.475][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-05-04 16:06:57.476][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-05-04 16:06:57.477][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-05-04 16:06:57.478][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-05-04 16:06:57.479][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-05-04 16:06:57.480][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-05-04 16:06:57.481][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:06:57.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:06:57.483][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:06:57.484][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-05-04 16:06:57.485][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-05-04 16:06:57.486][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:06:57.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:06:57.488][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:06:57.489][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-05-04 16:06:57.490][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-05-04 16:06:57.491][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:06:57.492][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:06:57.493][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:06:57.494][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-05-04 16:06:57.495][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-05-04 16:06:57.496][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:06:57.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:06:57.497][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:06:57.498][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-05-04 16:06:57.499][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-05-04 16:06:57.500][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:06:57.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:06:57.502][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:06:57.503][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-05-04 16:06:57.504][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-05-04 16:06:57.505][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:06:57.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:06:57.507][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:06:57.508][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-05-04 16:06:57.509][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-05-04 16:06:57.513][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-05-04 16:06:57.513][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:06:57.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:06:57.515][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:06:57.516][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-05-04 16:06:57.517][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-05-04 16:06:57.518][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-05-04 16:06:57.519][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:06:57.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:06:57.521][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:06:57.525][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-05-04 16:06:57.561][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-04 16:06:57.583][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-05-04 16:06:57.584][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-04 16:06:57.585][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-04 16:06:57.586][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-04 16:06:57.587][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-04 16:06:57.588][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-04 16:06:57.588][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-04 16:06:57.589][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-04 16:06:57.590][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-04 16:06:57.591][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-04 16:06:57.592][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-05-04 16:06:57.593][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-04 16:06:57.594][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:06:57.595][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-04 16:06:57.596][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-04 16:06:57.596][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-04 16:06:57.596][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-04 16:06:57.596][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-04 16:06:57.596][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-04 16:06:57.597][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-04 16:06:57.597][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:06:57.598][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:06:57.599][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-04 16:06:57.600][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:06:57.601][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:06:57.602][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-04 16:06:57.602][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:06:57.603][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-04 16:06:57.604][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-04 16:06:57.605][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-04 16:06:57.606][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:06:57.607][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-05-04 16:06:57.608][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-04 16:06:57.609][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-05-04 16:06:57.610][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-04 16:06:57.611][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-04 16:06:57.612][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-04 16:06:57.613][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-04 16:06:57.614][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-04 16:06:57.615][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-04 16:06:57.616][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-04 16:06:57.616][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-04 16:06:57.617][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-04 16:06:57.618][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-05-04 16:06:57.619][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-04 16:06:57.620][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:06:57.621][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-04 16:06:57.622][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-04 16:06:57.622][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-04 16:06:57.622][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-04 16:06:57.622][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-04 16:06:57.622][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-04 16:06:57.623][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-04 16:06:57.624][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:06:57.624][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:06:57.625][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-04 16:06:57.626][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:06:57.627][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:06:57.628][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-04 16:06:57.629][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:06:57.630][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-04 16:06:57.630][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-04 16:06:57.631][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-04 16:06:57.632][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:06:57.633][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-05-04 16:06:57.635][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-04 16:06:57.636][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-05-04 16:06:57.637][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-04 16:06:57.637][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-04 16:06:57.638][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-04 16:06:57.639][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-04 16:06:57.640][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-04 16:06:57.641][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-04 16:06:57.642][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-04 16:06:57.643][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-04 16:06:57.644][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-04 16:06:57.645][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-05-04 16:06:57.645][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-04 16:06:57.646][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:06:57.647][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-04 16:06:57.648][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:06:57.649][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-04 16:06:57.650][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:06:57.651][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:06:57.652][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-04 16:06:57.652][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:06:57.653][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:06:57.654][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-04 16:06:57.655][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:06:57.656][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-04 16:06:57.657][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-04 16:06:57.657][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-04 16:06:57.658][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:06:57.659][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-05-04 16:06:57.661][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-04 16:06:57.662][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-05-04 16:06:57.663][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-04 16:06:57.664][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-04 16:06:57.664][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-04 16:06:57.665][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-04 16:06:57.666][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-04 16:06:57.667][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-04 16:06:57.668][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-04 16:06:57.669][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-04 16:06:57.670][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-04 16:06:57.671][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-05-04 16:06:57.672][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-04 16:06:57.672][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:06:57.673][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-04 16:06:57.674][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:06:57.675][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-04 16:06:57.676][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:06:57.677][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:06:57.678][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-04 16:06:57.678][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:06:57.679][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:06:57.680][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-04 16:06:57.681][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:06:57.682][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-04 16:06:57.683][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-04 16:06:57.684][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-04 16:06:57.684][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:06:57.688][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-04 16:06:57.689][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:06:57.690][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:06:57.691][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:06:57.691][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:06:57.692][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:06:57.693][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:06:57.694][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:06:57.695][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:06:57.695][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:06:57.696][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:06:57.697][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:06:57.698][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:06:57.699][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:06:57.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:06:57.700][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:06:57.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:06:57.702][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:06:57.703][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:06:57.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:06:57.704][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:06:57.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:06:57.706][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:06:57.707][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:06:57.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:06:57.708][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:06:57.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:06:57.710][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:06:57.710][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:06:57.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:06:57.712][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:06:57.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:06:57.714][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:06:57.714][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:06:57.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:06:57.716][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:06:57.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:06:57.718][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:06:57.718][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:06:57.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:06:57.720][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:06:57.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:06:57.722][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:06:57.722][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:06:57.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:06:57.724][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:06:57.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:06:57.726][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:06:57.726][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:06:57.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:06:57.728][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:06:57.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:06:57.730][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:06:57.730][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:06:57.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:06:57.732][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:06:57.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:06:57.734][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:06:57.734][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:06:57.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:06:57.736][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:06:57.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:06:57.738][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:06:57.738][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:06:57.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:06:57.740][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:06:57.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:06:57.742][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:06:57.742][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:06:57.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:06:57.744][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:06:57.745][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:06:57.746][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:06:57.746][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:06:57.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:06:57.748][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:06:57.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:06:57.750][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:06:57.750][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:06:57.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:06:57.752][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:06:57.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:06:57.754][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:06:57.754][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:06:57.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:06:57.756][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:06:57.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:06:57.758][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:06:57.758][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-05-04 16:06:57.763][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-05-04 16:06:57.764][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-05-04 16:06:57.765][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-05-04 16:06:57.767][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-04 16:06:57.768][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-05-04 16:06:57.769][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-05-04 16:06:57.770][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-05-04 16:06:57.771][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-05-04 16:06:57.773][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-05-04 16:06:57.774][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-04 16:06:57.775][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-05-04 16:06:57.776][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-05-04 16:06:57.778][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-05-04 16:06:57.779][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-05-04 16:06:57.780][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-04 16:06:57.781][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-05-04 16:06:57.782][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-05-04 16:06:57.784][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-04 16:06:57.785][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-05-04 16:06:57.786][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-05-04 16:06:57.788][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-05-04 16:06:57.789][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-05-04 16:06:57.790][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-05-04 16:06:57.792][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-05-04 16:06:57.793][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-05-04 16:06:57.794][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-05-04 16:06:57.795][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-05-04 16:06:57.797][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-05-04 16:06:57.798][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-05-04 16:06:57.799][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-05-04 16:06:57.804][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-05-04 16:06:57.806][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-05-04 16:06:57.808][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-05-04 16:06:57.809][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-05-04 16:06:57.811][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-05-04 16:06:57.812][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-05-04 16:06:57.827][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-05-04 16:06:57.829][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-05-04 16:06:57.830][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-05-04 16:06:57.831][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-05-04 16:06:57.833][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-05-04 16:06:57.834][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-05-04 16:06:57.835][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-05-04 16:06:57.837][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-05-04 16:06:57.838][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-05-04 16:06:57.840][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-05-04 16:06:57.841][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-05-04 16:06:57.842][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-05-04 16:06:57.844][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-05-04 16:06:57.845][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-05-04 16:06:57.847][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-05-04 16:06:57.848][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-05-04 16:06:57.849][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-05-04 16:06:57.851][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-05-04 16:06:57.852][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-05-04 16:06:57.854][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-05-04 16:06:57.855][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-05-04 16:06:57.856][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-05-04 16:06:57.858][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-05-04 16:06:57.859][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-05-04 16:06:57.860][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-05-04 16:06:57.862][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-05-04 16:06:57.863][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-05-04 16:06:57.865][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-05-04 16:06:57.866][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-05-04 16:06:57.867][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-04 16:06:57.869][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-04 16:06:57.870][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-05-04 16:06:57.871][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-05-04 16:06:57.873][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-05-04 16:06:57.874][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-05-04 16:06:57.875][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-05-04 16:06:57.877][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-05-04 16:06:57.878][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-05-04 16:06:57.880][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-05-04 16:06:57.881][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-05-04 16:06:57.882][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-05-04 16:06:57.884][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-05-04 16:06:57.885][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-05-04 16:06:57.886][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-05-04 16:06:57.888][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-05-04 16:06:57.889][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-05-04 16:06:57.895][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-05-04 16:06:57.897][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-05-04 16:06:57.900][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-04 16:06:57.901][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:06:57.902][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:06:57.903][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:06:57.903][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:06:57.908][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:06:57.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:06:57.910][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:06:57.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:06:57.911][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:06:57.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:06:57.913][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[2024-05-04 16:06:57.914][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:06:57.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:06:57.916][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:06:57.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:06:57.917][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:06:57.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:06:57.919][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:06:57.920][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:06:57.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:06:57.922][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:06:57.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:06:57.923][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:06:57.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:06:57.925][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:06:57.926][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:06:57.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:06:57.928][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:06:57.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:06:57.929][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:06:57.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:06:57.931][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:06:57.932][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:06:57.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:06:57.934][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:06:57.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:06:57.935][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:06:57.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:06:57.937][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:06:57.938][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:06:57.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:06:57.940][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:06:57.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:06:57.941][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:06:57.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:06:57.943][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:06:57.944][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:06:57.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:06:57.946][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:06:57.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:06:57.947][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:06:57.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:06:57.949][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:06:57.950][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:06:57.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:06:57.952][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:06:57.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:06:57.953][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:06:57.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:06:57.955][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:06:57.956][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:06:57.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:06:57.958][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:06:57.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:06:57.959][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:06:57.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:06:57.961][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:06:57.962][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:06:57.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:06:57.964][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:06:57.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:06:57.966][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:06:57.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:06:57.967][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:06:57.968][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:06:57.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:06:57.970][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:06:57.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:06:57.972][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:06:57.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:06:57.973][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:06:57.974][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:06:57.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:06:57.976][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:06:57.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:06:57.978][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:06:57.978][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:06:57.979][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:06:57.980][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:06:57.981][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:06:57.982][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:06:57.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:06:57.984][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:06:57.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:06:57.985][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:06:57.986][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:06:57.987][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:06:57.988][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:06:57.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:06:57.990][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:06:57.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:06:57.991][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:06:57.992][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:06:57.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:06:57.994][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:06:57.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:06:57.996][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:06:57.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:06:57.997][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:06:57.998][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:06:57.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:06:58.000][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:06:58.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:06:58.002][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:06:58.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:06:58.003][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:06:58.004][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:06:58.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:06:58.006][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:06:58.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:06:58.008][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:06:58.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:06:58.009][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:06:58.011][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/definitions.yml".
biodb.DEBUG[2024-05-04 16:06:58.020][self$getDbsInfo()$define] Define connector expasy.enzyme.
biodb.DEBUG[2024-05-04 16:06:58.022][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-04 16:06:58.023][self$setPropertyValue] Setting property "description" to "Write here the description of this database.".
biodb.DEBUG[2024-05-04 16:06:58.024][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-04 16:06:58.024][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-04 16:06:58.025][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-04 16:06:58.026][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-04 16:06:58.027][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-05-04 16:06:58.028][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-04 16:06:58.029][self$setPropertyValue] Setting property "entry.content.type" to "txt".
biodb.DEBUG[2024-05-04 16:06:58.030][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-04 16:06:58.031][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-04 16:06:58.032][self$setPropertyValue] Setting property "name" to "Expasy ENZYME database.".
biodb.DEBUG[2024-05-04 16:06:58.033][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-04 16:06:58.034][self$setPropertyValue] Setting property "parsing.expr" to "^ID\s+([0-9.]+)$".
biodb.DEBUG[2024-05-04 16:06:58.034][self$setPropertyValue] Setting property "parsing.expr" to "^CA\s+(.+?)\.?$".
biodb.DEBUG[2024-05-04 16:06:58.034][self$setPropertyValue] Setting property "parsing.expr" to "^CF\s+(.+?)\.?$".
biodb.DEBUG[2024-05-04 16:06:58.034][self$setPropertyValue] Setting property "parsing.expr" to "^DE\s+(.+?)\.?$".
biodb.DEBUG[2024-05-04 16:06:58.035][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-05-04 16:06:58.036][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-04 16:06:58.037][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-05-04 16:06:58.038][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:06:58.039][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:06:58.039][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-04 16:06:58.040][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:06:58.041][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:06:58.042][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-04 16:06:58.043][self$setPropertyValue] Setting property "urls" to "https://enzyme.expasy.org/".
biodb.DEBUG[2024-05-04 16:06:58.044][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-04 16:06:58.045][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-04 16:06:58.046][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-05-04 16:06:58.047][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:06:58.052][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-05-04 16:06:58.078][super$initialize] Initialize connector expasy.enzyme.
biodb.DEBUG[2024-05-04 16:06:58.079][super$initialize] Register connector expasy.enzyme with the request scheduler
biodb.DEBUG[2024-05-04 16:06:58.083][private$bdb$getRequestScheduler()$re ...] Register connector expasy.enzyme.
biodb.DEBUG[2024-05-04 16:06:58.087][private$addConnectorRules] Create new rule for URL "enzyme.expasy.org" of connector "expasy.enzyme".
biodb.DEBUG[2024-05-04 16:06:58.091][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-04 16:06:58.092][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-04 16:06:58.093][biodb$getFactory()$createConn] Creating new connector expasy.enzyme for database class expasy.enzyme .
biodb.INFO [2024-05-04 16:06:58.102][biodb::testThat]
biodb.INFO [2024-05-04 16:06:58.102][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-05-04 16:06:58.103][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 16:06:58.104][biodb::testThat]
biodb.TRACE[2024-05-04 16:06:58.107][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.19-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/testref/entry-expasy.enzyme-1.1.1.1-content.txt".
biodb.DEBUG[2024-05-04 16:06:58.109][biodb$getFactory()$createEntryFromCo ...] Creating Expasy ENZYME database. entries from 1 content(s).
biodb.DEBUG[2024-05-04 16:06:58.112][biodb$getFactory()$createEntryFromCo ...] Parsing 1 Expasy ENZYME database. entries.
biodb.DEBUG[2024-05-04 16:06:58.121][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 16:06:58.122][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:06:58.122][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:06:58.133][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:06:58.134][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:06:58.135][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:06:58.136][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-04 16:06:58.146][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:06:58.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:06:58.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.173][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-05-04 16:06:58.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-05-04 16:06:58.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.186][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-05-04 16:06:58.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-05-04 16:06:58.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.190][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:06:58.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:06:58.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.194][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-05-04 16:06:58.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-05-04 16:06:58.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.198][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-05-04 16:06:58.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-05-04 16:06:58.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.201][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-05-04 16:06:58.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-05-04 16:06:58.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.205][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-05-04 16:06:58.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-05-04 16:06:58.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.209][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-05-04 16:06:58.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-05-04 16:06:58.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.227][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:06:58.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:06:58.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.230][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:06:58.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:06:58.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.263][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:06:58.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:06:58.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.266][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:06:58.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:06:58.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.270][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:06:58.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:06:58.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.274][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-05-04 16:06:58.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-05-04 16:06:58.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.277][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-05-04 16:06:58.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-05-04 16:06:58.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.281][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:06:58.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:06:58.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.285][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-05-04 16:06:58.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-05-04 16:06:58.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.288][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:06:58.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:06:58.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.298][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:06:58.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:06:58.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.302][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:06:58.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:06:58.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.306][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:06:58.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:06:58.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.310][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:06:58.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:06:58.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.313][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:06:58.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:06:58.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 16:06:58.317][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 1.1.1.1.
biodb.TRACE[2024-05-04 16:06:58.320][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-04 16:06:58.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-04 16:06:58.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.323][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-04 16:06:58.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-04 16:06:58.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.327][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-04 16:06:58.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-04 16:06:58.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.330][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-04 16:06:58.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-04 16:06:58.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.347][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:06:58.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:06:58.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.361][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-05-04 16:06:58.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-05-04 16:06:58.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.367][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:06:58.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:06:58.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.371][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:06:58.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:06:58.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.374][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:06:58.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:06:58.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.379][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:06:58.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:06:58.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.383][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:06:58.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:06:58.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.387][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:06:58.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:06:58.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.390][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-05-04 16:06:58.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-05-04 16:06:58.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.394][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-05-04 16:06:58.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-05-04 16:06:58.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.397][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-05-04 16:06:58.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-05-04 16:06:58.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.406][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:06:58.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:06:58.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.410][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:06:58.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:06:58.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.413][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:06:58.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:06:58.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.417][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:06:58.418][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:06:58.419][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.420][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.421][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:06:58.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:06:58.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.431][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:06:58.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:06:58.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.434][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:06:58.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:06:58.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.438][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:06:58.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:06:58.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.441][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:06:58.442][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:06:58.443][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.444][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.445][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:06:58.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:06:58.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.454][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-05-04 16:06:58.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-05-04 16:06:58.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.458][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-05-04 16:06:58.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-05-04 16:06:58.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.461][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-05-04 16:06:58.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-05-04 16:06:58.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.465][ef$get] Asked field names are: cofactor.
biodb.TRACE[2024-05-04 16:06:58.466][ef$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-05-04 16:06:58.467][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.468][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.468][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-05-04 16:06:58.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-05-04 16:06:58.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.478][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-05-04 16:06:58.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-05-04 16:06:58.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.481][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-05-04 16:06:58.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-05-04 16:06:58.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.485][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-05-04 16:06:58.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-05-04 16:06:58.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.489][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-05-04 16:06:58.490][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-05-04 16:06:58.491][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.492][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.493][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-05-04 16:06:58.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-05-04 16:06:58.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.522][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:06:58.523][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:06:58.524][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.525][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.528][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-05-04 16:06:58.529][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-05-04 16:06:58.530][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.531][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.534][ef$get] Asked field names are: cofactor.
biodb.TRACE[2024-05-04 16:06:58.535][ef$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-05-04 16:06:58.536][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.537][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.541][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:06:58.542][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:06:58.542][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.543][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.558][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.19-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/testref/entry-expasy.enzyme-1.1.1.54-content.txt".
biodb.DEBUG[2024-05-04 16:06:58.589][biodb$getFactory()$createEntryFromCo ...] Creating Expasy ENZYME database. entries from 1 content(s).
biodb.DEBUG[2024-05-04 16:06:58.590][biodb$getFactory()$createEntryFromCo ...] Parsing 1 Expasy ENZYME database. entries.
biodb.DEBUG[2024-05-04 16:06:58.591][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 16:06:58.592][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:06:58.593][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:06:58.596][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:06:58.597][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:06:58.598][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:06:58.599][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-04 16:06:58.600][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:06:58.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:06:58.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.604][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-05-04 16:06:58.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-05-04 16:06:58.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.608][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:06:58.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:06:58.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.612][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-05-04 16:06:58.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-05-04 16:06:58.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.615][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-05-04 16:06:58.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-05-04 16:06:58.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.619][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-05-04 16:06:58.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-05-04 16:06:58.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.622][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:06:58.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:06:58.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.626][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-05-04 16:06:58.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-05-04 16:06:58.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.630][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:06:58.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:06:58.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.633][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:06:58.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:06:58.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.637][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:06:58.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:06:58.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.640][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:06:58.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:06:58.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.644][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:06:58.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:06:58.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.648][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:06:58.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:06:58.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 16:06:58.651][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 1.1.1.54.
biodb.TRACE[2024-05-04 16:06:58.669][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-04 16:06:58.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-04 16:06:58.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.672][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-04 16:06:58.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-04 16:06:58.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.676][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-04 16:06:58.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-04 16:06:58.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.679][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-04 16:06:58.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-04 16:06:58.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.683][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:06:58.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:06:58.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.690][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-05-04 16:06:58.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-05-04 16:06:58.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.699][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:06:58.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:06:58.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.703][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:06:58.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:06:58.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.706][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:06:58.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:06:58.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.711][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:06:58.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:06:58.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.714][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:06:58.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:06:58.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.718][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:06:58.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:06:58.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.722][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-05-04 16:06:58.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-05-04 16:06:58.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.725][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-05-04 16:06:58.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-05-04 16:06:58.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.729][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-05-04 16:06:58.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-05-04 16:06:58.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.745][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:06:58.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:06:58.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.749][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:06:58.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:06:58.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.752][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:06:58.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:06:58.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.756][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:06:58.757][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:06:58.758][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.759][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.760][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:06:58.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:06:58.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.769][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:06:58.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:06:58.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.772][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:06:58.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:06:58.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.776][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:06:58.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:06:58.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.780][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:06:58.781][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:06:58.781][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.782][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.783][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:06:58.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:06:58.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.792][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-05-04 16:06:58.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-05-04 16:06:58.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.796][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-05-04 16:06:58.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-05-04 16:06:58.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.800][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-05-04 16:06:58.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-05-04 16:06:58.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.803][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-05-04 16:06:58.804][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-05-04 16:06:58.805][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.806][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.807][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-05-04 16:06:58.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-05-04 16:06:58.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.816][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:06:58.817][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:06:58.818][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.819][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.822][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-05-04 16:06:58.823][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-05-04 16:06:58.824][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.825][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:06:58.828][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:06:58.829][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:06:58.830][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:06:58.831][ef$get] fields variable is a list.
biodb.INFO [2024-05-04 16:06:58.837][biodb::testThat]
biodb.INFO [2024-05-04 16:06:58.838][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-05-04 16:06:58.839][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 16:06:58.839][biodb::testThat]
biodb.DEBUG[2024-05-04 16:06:58.841][private$loadEntries] Creating entries from ids [2]: "1.1.1.1, 1.1.1.54".
biodb.DEBUG[2024-05-04 16:06:58.848][conn$getEntryContent] Get Expasy ENZYME database. entry content(s) for 2 id(s)...
biodb.TRACE[2024-05-04 16:06:58.852][cch$loadFileContent] Trying to load 2 files from cache: [2]: "1.1.1.1, 1.1.1.54".
biodb.TRACE[2024-05-04 16:06:58.853][cch$loadFileContent] file.exist = [2]: "TRUE, FALSE".
biodb.TRACE[2024-05-04 16:06:58.854][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/1.1.1.1.txt".
biodb.DEBUG[2024-05-04 16:06:58.855][conn$getEntryContent] 1 Expasy ENZYME database. entry content(s) loaded from cache.
biodb.DEBUG[2024-05-04 16:06:58.856][conn$getEntryContent] 1 entry content(s) need to be fetched from Expasy ENZYME database. database "https://enzyme.expasy.org/".
biodb.DEBUG[2024-05-04 16:06:58.857][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-04 16:06:58.858][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-04 16:06:58.863][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 16:06:58.863][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:06:58.864][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:06:58.868][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:06:58.869][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:06:58.869][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:06:58.870][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:06:58.871][scheduler$sendRequest] Getting content of get URL request "https://enzyme.expasy.org/EC/1.1.1.54.txt".
biodb.DEBUG[2024-05-04 16:06:58.893][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 16:06:58.894][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-04 16:06:58.895][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/EC/1.1.1.54.txt".
biodb.TRACE[2024-05-04 16:06:59.836][getRCurlRequestResult] Using RCurl package for sending request (https://enzyme.expasy.org/EC/1.1.1.54.txt).
biodb.DEBUG[2024-05-04 16:07:00.637][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-04 16:07:00.642][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a9b93566a091cbe35a06e4b3871f95c9.content"
biodb.TRACE[2024-05-04 16:07:00.675][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a9b93566a091cbe35a06e4b3871f95c9.request"
biodb.TRACE[2024-05-04 16:07:00.680][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/1.1.1.54.txt"
biodb.DEBUG[2024-05-04 16:07:00.683][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-04 16:07:00.685][self$createEntryFromContent] Creating Expasy ENZYME database. entries from 2 content(s).
biodb.DEBUG[2024-05-04 16:07:00.687][self$createEntryFromContent] Parsing 2 Expasy ENZYME database. entries.
biodb.DEBUG[2024-05-04 16:07:00.690][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 16:07:00.691][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:00.693][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:00.699][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:00.700][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:00.702][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:00.703][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-04 16:07:00.706][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:00.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:00.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:00.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:00.712][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-05-04 16:07:00.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-05-04 16:07:00.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:00.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:00.717][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:07:00.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:07:00.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:00.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:00.721][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-05-04 16:07:00.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-05-04 16:07:00.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:00.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:00.726][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:07:00.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:07:00.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:00.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:00.730][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:07:00.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:07:00.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:00.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:00.734][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:07:00.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:07:00.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:00.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:00.738][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:07:00.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:07:00.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:00.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:00.742][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:07:00.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:07:00.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:00.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:00.746][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-05-04 16:07:00.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-05-04 16:07:00.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:00.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:00.750][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-05-04 16:07:00.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-05-04 16:07:00.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:00.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:00.754][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:00.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:00.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:00.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:00.758][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-05-04 16:07:00.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-05-04 16:07:00.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:00.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:00.762][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:00.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:00.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:00.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:00.776][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:00.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:00.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:00.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:00.782][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:00.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:00.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:00.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 16:07:00.786][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-04 16:07:00.787][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:00.788][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:00.792][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:00.793][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:00.794][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:00.795][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-04 16:07:00.797][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:00.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:00.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:00.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:00.802][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-05-04 16:07:00.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-05-04 16:07:00.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:00.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:00.806][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:07:00.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:07:00.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:00.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:00.810][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-05-04 16:07:00.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-05-04 16:07:00.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:00.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:00.814][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-05-04 16:07:00.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-05-04 16:07:00.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:00.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:00.818][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-05-04 16:07:00.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-05-04 16:07:00.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:00.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:00.822][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:00.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:00.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:00.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:00.826][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-05-04 16:07:00.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-05-04 16:07:00.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:00.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:00.830][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:00.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:00.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:00.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:00.834][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:00.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:00.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:00.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:00.838][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:00.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:00.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:00.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:00.843][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:00.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:00.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:00.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:00.847][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:00.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:00.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:00.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:00.850][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:00.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:00.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:00.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:00.854][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:00.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:00.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:00.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:00.858][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:00.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:00.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:00.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:00.862][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-04 16:07:00.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-04 16:07:00.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:00.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 16:07:00.866][self$createEntryFromContent] Accession numbers: 1.1.1.1, 1.1.1.54.
biodb.TRACE[2024-05-04 16:07:00.867][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-05-04 16:07:00.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-05-04 16:07:00.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:00.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:00.871][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-05-04 16:07:00.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-05-04 16:07:00.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:00.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:00.875][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-05-04 16:07:00.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-05-04 16:07:00.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:00.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:00.883][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-05-04 16:07:00.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-05-04 16:07:00.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:00.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:00.887][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-05-04 16:07:00.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-05-04 16:07:00.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:00.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:00.891][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-05-04 16:07:00.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-05-04 16:07:00.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:00.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-04 16:07:00.901][biodb::testThat]
biodb.INFO [2024-05-04 16:07:00.902][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-05-04 16:07:00.903][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 16:07:00.904][biodb::testThat]
biodb.TRACE[2024-05-04 16:07:00.907][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:07:00.908][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:07:00.909][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:00.910][ef$get] fields variable is a list.
biodb.DEBUG[2024-05-04 16:07:00.911][function(conn, opt)] Testing searchForEntries() with entry "1.1.1.1" and field "name".
biodb.TRACE[2024-05-04 16:07:00.935][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:07:00.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:07:00.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:00.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:00.939][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:07:00.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:07:00.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:00.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:00.943][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:07:00.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:07:00.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:00.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 16:07:00.950][function(conn, opt)] With value "alcohol dehydrogenase".
biodb.DEBUG[2024-05-04 16:07:00.976][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://enzyme.expasy.org/enzyme-byname.html?alcohol dehydrogenase".
biodb.DEBUG[2024-05-04 16:07:00.991][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-04 16:07:00.992][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-04 16:07:01.007][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase".
biodb.TRACE[2024-05-04 16:07:01.711][getRCurlRequestResult] Using RCurl package for sending request (https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase).
biodb.DEBUG[2024-05-04 16:07:02.626][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-04 16:07:02.632][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.content"
biodb.TRACE[2024-05-04 16:07:02.642][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.request"
biodb.DEBUG[2024-05-04 16:07:02.664][function(conn, opt)] With found IDs [1]: "1.1.1.1".
biodb.INFO [2024-05-04 16:07:02.694][biodb::testThat]
biodb.INFO [2024-05-04 16:07:02.696][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-05-04 16:07:02.697][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 16:07:02.699][biodb::testThat]
biodb.TRACE[2024-05-04 16:07:02.733][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:07:02.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:07:02.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:02.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:02.738][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:07:02.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:07:02.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:02.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:02.743][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:07:02.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:07:02.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:02.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-04 16:07:02.783][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://enzyme.expasy.org/enzyme-byname.html?alcohol dehydrogenase".
biodb.DEBUG[2024-05-04 16:07:02.794][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-04 16:07:02.814][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f603fa2a57aec59588edc37541c6f6d5".
biodb.TRACE[2024-05-04 16:07:02.815][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-04 16:07:02.817][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.content".
biodb.INFO [2024-05-04 16:07:02.857][biodb::testThat]
biodb.INFO [2024-05-04 16:07:02.858][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-05-04 16:07:02.859][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 16:07:02.860][biodb::testThat]
biodb.TRACE[2024-05-04 16:07:02.871][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-04 16:07:02.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-04 16:07:02.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:02.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:02.875][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-04 16:07:02.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-04 16:07:02.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:02.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:02.879][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-04 16:07:02.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-04 16:07:02.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:02.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:02.883][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-04 16:07:02.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-04 16:07:02.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:02.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:02.918][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-04 16:07:02.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-04 16:07:02.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:02.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:02.921][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-04 16:07:02.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-04 16:07:02.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:02.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:02.925][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-04 16:07:02.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-04 16:07:02.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:02.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:02.929][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-04 16:07:02.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-04 16:07:02.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:02.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-04 16:07:02.937][biodb::testThat]
biodb.INFO [2024-05-04 16:07:02.938][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-05-04 16:07:02.939][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 16:07:02.940][biodb::testThat]
biodb.INFO [2024-05-04 16:07:02.948][biodb::testThat]
biodb.INFO [2024-05-04 16:07:02.948][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-05-04 16:07:02.949][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 16:07:02.950][biodb::testThat]
biodb.INFO [2024-05-04 16:07:02.957][biodb::testThat]
biodb.INFO [2024-05-04 16:07:02.958][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-05-04 16:07:02.959][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 16:07:02.960][biodb::testThat]
biodb.DEBUG[2024-05-04 16:07:02.972][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[2024-05-04 16:07:03.656][getUrlContent] Use RCurl 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 [2024-05-04 16:07:04.419][biodb::testThat]
biodb.INFO [2024-05-04 16:07:04.421][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-05-04 16:07:04.423][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-04 16:07:04.425][biodb::testThat]
biodb.DEBUG[2024-05-04 16:07:05.896][getUrlContent] Use RCurl for downloading content of URL https://enzyme.expasy.org/images/1.1.1.1/image.png.
biodb.TRACE[2024-05-04 16:07:06.310][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:07:06.312][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:07:06.314][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:06.316][ef$get] fields variable is a list.
biodb.TRACE[2024-05-04 16:07:06.319][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-04 16:07:06.321][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-04 16:07:06.323][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-04 16:07:06.325][ef$get] fields variable is a list.
biodb.INFO [2024-05-04 16:07:06.328][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-05-04 16:07:06.330][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector expasy.enzyme from the request scheduler
biodb.INFO [2024-05-04 16:07:06.333][self$deleteConn] Connector "expasy.enzyme" deleted.
biodb.DEBUG[2024-05-04 16:07:06.335][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-05-04 16:07:06.337][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:06.339][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:06.341][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:06.343][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:06.345][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:06.347][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-05-04 16:07:06.375][biodb::testContext]
biodb.INFO [2024-05-04 16:07:06.376][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-04 16:07:06.377][biodb::testContext] Test context - Example long tests
biodb.INFO [2024-05-04 16:07:06.378][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-04 16:07:06.379][biodb::testContext]
biodb.INFO [2024-05-04 16:07:06.382][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-05-04 16:07:06.384][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-05-04 16:07:06.388][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-04 16:07:06.389][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-05-04 16:07:06.390][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-05-04 16:07:06.391][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:06.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:06.393][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:06.394][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-05-04 16:07:06.395][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-05-04 16:07:06.395][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:06.396][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:06.397][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:06.398][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-05-04 16:07:06.399][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-05-04 16:07:06.400][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:06.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:06.402][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:06.402][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-05-04 16:07:06.403][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-05-04 16:07:06.404][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-05-04 16:07:06.405][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:06.406][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:06.407][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:06.408][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-05-04 16:07:06.409][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-05-04 16:07:06.409][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-05-04 16:07:06.410][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:06.411][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:06.412][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:06.413][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-05-04 16:07:06.414][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-05-04 16:07:06.414][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:06.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:06.416][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:06.417][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-05-04 16:07:06.418][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-05-04 16:07:06.419][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-05-04 16:07:06.420][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:06.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:06.421][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:06.422][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-05-04 16:07:06.423][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-05-04 16:07:06.424][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:06.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:06.425][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:06.426][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-05-04 16:07:06.427][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-05-04 16:07:06.428][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-05-04 16:07:06.429][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:06.430][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:06.431][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:06.431][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-05-04 16:07:06.432][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-05-04 16:07:06.433][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-05-04 16:07:06.434][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-05-04 16:07:06.435][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-05-04 16:07:06.436][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-05-04 16:07:06.437][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:06.438][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:06.438][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:06.439][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-05-04 16:07:06.440][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-05-04 16:07:06.441][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:06.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:06.443][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:06.444][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-05-04 16:07:06.444][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-05-04 16:07:06.445][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:06.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:06.447][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:06.448][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-05-04 16:07:06.449][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-05-04 16:07:06.450][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:06.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:06.451][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:06.452][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-05-04 16:07:06.453][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-05-04 16:07:06.454][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:06.455][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:06.455][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:06.456][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-05-04 16:07:06.457][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-05-04 16:07:06.458][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:06.459][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:06.460][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:06.460][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-05-04 16:07:06.461][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-05-04 16:07:06.464][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-05-04 16:07:06.465][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:06.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:06.467][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:06.468][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-05-04 16:07:06.468][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-05-04 16:07:06.469][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-05-04 16:07:06.470][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:06.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:06.472][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:06.473][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-05-04 16:07:06.474][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-04 16:07:06.475][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-05-04 16:07:06.476][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:06.477][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-04 16:07:06.478][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:06.479][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-04 16:07:06.480][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-04 16:07:06.481][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-04 16:07:06.482][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-04 16:07:06.483][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-04 16:07:06.484][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:06.484][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-05-04 16:07:06.485][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-04 16:07:06.486][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:07:06.487][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:06.488][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-04 16:07:06.488][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-04 16:07:06.488][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-04 16:07:06.488][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-04 16:07:06.488][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-04 16:07:06.489][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-04 16:07:06.490][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:07:06.491][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:07:06.492][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-04 16:07:06.493][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:07:06.493][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:07:06.494][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-04 16:07:06.495][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:07:06.496][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-04 16:07:06.497][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-04 16:07:06.498][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-04 16:07:06.498][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:07:06.500][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-05-04 16:07:06.501][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-04 16:07:06.502][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-05-04 16:07:06.503][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:06.504][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-04 16:07:06.505][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:06.506][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-04 16:07:06.507][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-04 16:07:06.507][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-04 16:07:06.508][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-04 16:07:06.509][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-04 16:07:06.510][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:06.511][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-05-04 16:07:06.512][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-04 16:07:06.513][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:07:06.514][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:06.515][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-04 16:07:06.515][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-04 16:07:06.515][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-04 16:07:06.515][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-04 16:07:06.515][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-04 16:07:06.516][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-04 16:07:06.517][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:07:06.517][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:07:06.518][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-04 16:07:06.519][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:07:06.520][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:07:06.521][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-04 16:07:06.522][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:07:06.523][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-04 16:07:06.523][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-04 16:07:06.524][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-04 16:07:06.525][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:07:06.526][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-05-04 16:07:06.528][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:06.529][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-05-04 16:07:06.530][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:06.531][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-04 16:07:06.531][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:06.532][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-04 16:07:06.533][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-04 16:07:06.534][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-04 16:07:06.535][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-04 16:07:06.536][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-04 16:07:06.537][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-04 16:07:06.538][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-05-04 16:07:06.542][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-04 16:07:06.543][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:07:06.544][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:06.545][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:07:06.546][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-04 16:07:06.547][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:07:06.548][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:07:06.549][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-04 16:07:06.550][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:07:06.550][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:07:06.551][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-04 16:07:06.552][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:07:06.553][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-04 16:07:06.554][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-04 16:07:06.555][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-04 16:07:06.556][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:07:06.557][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-05-04 16:07:06.558][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:06.559][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-05-04 16:07:06.560][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:06.561][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-04 16:07:06.562][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:06.563][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-04 16:07:06.564][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-04 16:07:06.565][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-04 16:07:06.565][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-04 16:07:06.566][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-04 16:07:06.567][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-04 16:07:06.568][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-05-04 16:07:06.569][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-04 16:07:06.570][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:07:06.571][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:06.572][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:07:06.573][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-04 16:07:06.574][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:07:06.574][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:07:06.575][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-04 16:07:06.576][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:07:06.577][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:07:06.578][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-04 16:07:06.579][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:07:06.580][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-04 16:07:06.580][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-04 16:07:06.581][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-04 16:07:06.582][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:07:06.583][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-04 16:07:06.584][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:06.585][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:06.586][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:06.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:06.587][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:06.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:06.589][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[2024-05-04 16:07:06.590][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:06.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:06.591][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:06.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:06.593][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:06.594][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:06.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:06.595][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:06.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:06.597][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:06.598][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:06.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:06.599][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:06.600][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:06.601][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:06.602][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:06.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:06.603][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:06.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:06.605][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:06.606][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:06.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:06.607][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:06.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:06.609][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[2024-05-04 16:07:06.610][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:06.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:06.611][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:06.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:06.613][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:06.614][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:06.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:06.616][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:06.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:06.617][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:06.618][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:06.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:06.620][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:06.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:06.621][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:06.622][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:06.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:06.624][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:06.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:06.625][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[2024-05-04 16:07:06.626][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:06.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:06.628][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:06.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:06.630][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[2024-05-04 16:07:06.630][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:06.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:06.632][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:06.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:06.634][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:06.635][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:06.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:06.636][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:06.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:06.638][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:06.639][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:06.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:06.641][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:06.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:06.642][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:06.643][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:06.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:06.645][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:06.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:06.647][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:06.648][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:06.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:06.649][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:06.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:06.651][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:06.652][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:06.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:06.653][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:06.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:06.655][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:06.656][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-05-04 16:07:06.657][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-05-04 16:07:06.659][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-05-04 16:07:06.660][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-05-04 16:07:06.661][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-04 16:07:06.663][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-05-04 16:07:06.664][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-05-04 16:07:06.665][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-05-04 16:07:06.666][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-05-04 16:07:06.668][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-05-04 16:07:06.669][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-04 16:07:06.670][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-05-04 16:07:06.671][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-05-04 16:07:06.673][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-05-04 16:07:06.674][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-05-04 16:07:06.675][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-04 16:07:06.676][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-05-04 16:07:06.678][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-05-04 16:07:06.679][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-04 16:07:06.680][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-05-04 16:07:06.681][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-05-04 16:07:06.683][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-05-04 16:07:06.684][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-05-04 16:07:06.685][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-05-04 16:07:06.686][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-05-04 16:07:06.688][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-05-04 16:07:06.689][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-05-04 16:07:06.690][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-05-04 16:07:06.691][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-05-04 16:07:06.693][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-05-04 16:07:06.694][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-05-04 16:07:06.695][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-05-04 16:07:06.696][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-05-04 16:07:06.698][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-05-04 16:07:06.699][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-05-04 16:07:06.700][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-05-04 16:07:06.701][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-05-04 16:07:06.703][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-05-04 16:07:06.707][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-05-04 16:07:06.709][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-05-04 16:07:06.710][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-05-04 16:07:06.711][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-05-04 16:07:06.712][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-05-04 16:07:06.714][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-05-04 16:07:06.715][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-05-04 16:07:06.716][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-05-04 16:07:06.717][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-05-04 16:07:06.719][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-05-04 16:07:06.720][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-05-04 16:07:06.721][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-05-04 16:07:06.722][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-05-04 16:07:06.724][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-05-04 16:07:06.725][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-05-04 16:07:06.726][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-05-04 16:07:06.727][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-05-04 16:07:06.729][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-05-04 16:07:06.730][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-05-04 16:07:06.731][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-05-04 16:07:06.733][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-05-04 16:07:06.734][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-05-04 16:07:06.735][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-05-04 16:07:06.736][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-05-04 16:07:06.738][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-05-04 16:07:06.739][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-05-04 16:07:06.740][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-05-04 16:07:06.741][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-05-04 16:07:06.743][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-04 16:07:06.744][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-04 16:07:06.748][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-05-04 16:07:06.750][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-05-04 16:07:06.752][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-05-04 16:07:06.753][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-05-04 16:07:06.754][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-05-04 16:07:06.756][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-05-04 16:07:06.757][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-05-04 16:07:06.759][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-05-04 16:07:06.760][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-05-04 16:07:06.761][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-05-04 16:07:06.763][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-05-04 16:07:06.764][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-05-04 16:07:06.765][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-05-04 16:07:06.767][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-05-04 16:07:06.768][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-05-04 16:07:06.770][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-05-04 16:07:06.772][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-05-04 16:07:06.773][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-04 16:07:06.774][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:06.774][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:06.775][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:06.776][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:06.777][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:06.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:06.779][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:06.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:06.781][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:06.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:06.782][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:06.783][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:06.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:06.785][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:06.786][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:06.787][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:06.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:06.789][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:06.790][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:06.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:06.791][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:06.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:06.793][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:06.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:06.795][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:06.796][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:06.797][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:06.797][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:06.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:06.799][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:06.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:06.801][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:06.802][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:06.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:06.804][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:06.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:06.805][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:06.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:06.807][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:06.808][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:06.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:06.810][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:06.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:06.811][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:06.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:06.813][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:06.814][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:06.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:06.816][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:06.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:06.818][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:06.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:06.819][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:06.820][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:06.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:06.822][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:06.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:06.824][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:06.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:06.826][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:06.826][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:06.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:06.828][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:06.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:06.830][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:06.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:06.832][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:06.833][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:06.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:06.834][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:06.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:06.836][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:06.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:06.838][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:06.839][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:06.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:06.840][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:06.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:06.842][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:06.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:06.844][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:06.845][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:06.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:06.847][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:06.847][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:06.848][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:06.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:06.850][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:06.851][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:06.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:06.853][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:06.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:06.855][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:06.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:06.856][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:06.857][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:06.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:06.859][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:06.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:06.861][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:06.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:06.862][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:06.863][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:06.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:06.865][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:06.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:06.867][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:06.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:06.869][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:06.869][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:06.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:06.871][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:06.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:06.873][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:06.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:06.875][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:06.876][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-04 16:07:06.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:06.877][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:06.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:06.879][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:06.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:06.894][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-04 16:07:06.895][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/definitions.yml".
biodb.DEBUG[2024-05-04 16:07:06.897][self$getDbsInfo()$define] Define connector expasy.enzyme.
biodb.DEBUG[2024-05-04 16:07:06.899][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-04 16:07:06.899][self$setPropertyValue] Setting property "description" to "Write here the description of this database.".
biodb.DEBUG[2024-05-04 16:07:06.900][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:06.902][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-04 16:07:06.902][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:06.903][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-04 16:07:06.905][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:06.905][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-04 16:07:06.906][self$setPropertyValue] Setting property "entry.content.type" to "txt".
biodb.DEBUG[2024-05-04 16:07:06.907][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-04 16:07:06.908][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:06.909][self$setPropertyValue] Setting property "name" to "Expasy ENZYME database.".
biodb.DEBUG[2024-05-04 16:07:06.910][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-04 16:07:06.911][self$setPropertyValue] Setting property "parsing.expr" to "^ID\s+([0-9.]+)$".
biodb.DEBUG[2024-05-04 16:07:06.911][self$setPropertyValue] Setting property "parsing.expr" to "^CA\s+(.+?)\.?$".
biodb.DEBUG[2024-05-04 16:07:06.911][self$setPropertyValue] Setting property "parsing.expr" to "^CF\s+(.+?)\.?$".
biodb.DEBUG[2024-05-04 16:07:06.911][self$setPropertyValue] Setting property "parsing.expr" to "^DE\s+(.+?)\.?$".
biodb.DEBUG[2024-05-04 16:07:06.912][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-05-04 16:07:06.913][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-04 16:07:06.914][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-05-04 16:07:06.915][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:07:06.916][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:07:06.917][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-04 16:07:06.918][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-04 16:07:06.919][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-04 16:07:06.920][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-04 16:07:06.921][self$setPropertyValue] Setting property "urls" to "https://enzyme.expasy.org/".
biodb.DEBUG[2024-05-04 16:07:06.922][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-04 16:07:06.923][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-04 16:07:06.924][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-05-04 16:07:06.925][self$setPropertyValue]
biodb.DEBUG[2024-05-04 16:07:06.926][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-05-04 16:07:06.929][super$initialize] Initialize connector expasy.enzyme.
biodb.DEBUG[2024-05-04 16:07:06.930][super$initialize] Register connector expasy.enzyme with the request scheduler
biodb.DEBUG[2024-05-04 16:07:06.931][private$bdb$getRequestScheduler()$re ...] Register connector expasy.enzyme.
biodb.DEBUG[2024-05-04 16:07:06.933][private$addConnectorRules] Create new rule for URL "enzyme.expasy.org" of connector "expasy.enzyme".
biodb.DEBUG[2024-05-04 16:07:06.934][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-04 16:07:06.935][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-04 16:07:06.936][biodb$getFactory()$createConn] Creating new connector expasy.enzyme for database class expasy.enzyme .
biodb.INFO [2024-05-04 16:07:06.937][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-05-04 16:07:06.938][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector expasy.enzyme from the request scheduler
biodb.INFO [2024-05-04 16:07:06.939][self$deleteConn] Connector "expasy.enzyme" deleted.
biodb.DEBUG[2024-05-04 16:07:06.939][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-05-04 16:07:06.940][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-04 16:07:06.941][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-04 16:07:06.942][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-04 16:07:06.943][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-04 16:07:06.943][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-05-04 16:07:06.944][FUN] Functions in observer 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 0 | WARN 0 | SKIP 0 | PASS 85 ]
> 
> proc.time()
   user  system elapsed 
  5.121   0.268  11.175 

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbExpasy_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc-longtests/meat/biodbExpasy.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘biodbExpasy/DESCRIPTION’ ... OK
* this is package ‘biodbExpasy’ version ‘1.8.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... 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 loading without being on the library search path ... 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’
 OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.19-bioc-longtests/meat/biodbExpasy.Rcheck/00check.log’
for details.


Installation output

biodbExpasy.Rcheck/00install.out

* installing *source* package ‘biodbExpasy’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (biodbExpasy)