Back to Long Tests report for BioC 3.19

This page was generated on 2024-06-22 23:55 -0400 (Sat, 22 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4758
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4492
merida1macOS 12.7.4 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4506
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: 2024-06-22 09:55 -0400 (Sat, 22 Jun 2024)
git_url: https://git.bioconductor.org/packages/biodbExpasy
git_branch: RELEASE_3_19
git_last_commit: de004e8
git_last_commit_date: 2024-04-30 11:41:12 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  ERROR  
palomino3Windows Server 2022 Datacenter / x64  ERROR  
merida1macOS 12.7.4 Monterey / x86_64  ERROR  

CHECK results for biodbExpasy on merida1

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: /Library/Frameworks/R.framework/Resources/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: 2024-06-22 16:01:19 -0400 (Sat, 22 Jun 2024)
EndedAt: 2024-06-22 16:02:24 -0400 (Sat, 22 Jun 2024)
EllapsedTime: 64.7 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbExpasy.Rcheck
Warnings: NA

Tests output

biodbExpasy.Rcheck/tests/testthat.Rout.fail


R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbExpasy)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbExpasy")
biodb.INFO [2024-06-22 16:02:15.344][biodb::testContext]
biodb.INFO [2024-06-22 16:02:15.348][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-22 16:02:15.350][biodb::testContext] Test context - Generic long tests
biodb.INFO [2024-06-22 16:02:15.351][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-22 16:02:15.352][biodb::testContext]
biodb.INFO [2024-06-22 16:02:15.361][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-06-22 16:02:15.364][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-06-22 16:02:15.373][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-22 16:02:15.375][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-06-22 16:02:15.376][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-06-22 16:02:15.378][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:15.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:15.381][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:15.383][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-06-22 16:02:15.427][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-06-22 16:02:15.428][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:15.429][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:15.431][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[2024-06-22 16:02:15.432][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-06-22 16:02:15.433][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-06-22 16:02:15.434][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:15.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:15.436][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:15.438][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-06-22 16:02:15.439][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-06-22 16:02:15.440][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-06-22 16:02:15.441][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:15.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:15.443][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[2024-06-22 16:02:15.445][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-06-22 16:02:15.446][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-06-22 16:02:15.447][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-06-22 16:02:15.448][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:15.449][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:15.451][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:15.452][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-06-22 16:02:15.453][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-06-22 16:02:15.454][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:15.455][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:15.456][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:15.458][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-06-22 16:02:15.459][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-06-22 16:02:15.460][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-06-22 16:02:15.461][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:15.462][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:15.463][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:15.465][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-06-22 16:02:15.466][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-06-22 16:02:15.467][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:15.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:15.469][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:15.470][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-06-22 16:02:15.472][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-06-22 16:02:15.473][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-06-22 16:02:15.474][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:15.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:15.476][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:15.478][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-06-22 16:02:15.479][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-06-22 16:02:15.480][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-06-22 16:02:15.481][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-06-22 16:02:15.483][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-06-22 16:02:15.484][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-06-22 16:02:15.485][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:15.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:15.487][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:15.488][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-06-22 16:02:15.490][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-06-22 16:02:15.491][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:15.492][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:15.493][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:15.494][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-06-22 16:02:15.496][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-06-22 16:02:15.497][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:15.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:15.499][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:15.500][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-06-22 16:02:15.502][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-06-22 16:02:15.503][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:15.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:15.505][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:15.506][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-06-22 16:02:15.507][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-06-22 16:02:15.509][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:15.510][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:15.511][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:15.512][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-06-22 16:02:15.513][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-06-22 16:02:15.515][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:15.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:15.517][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:15.518][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-06-22 16:02:15.519][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-06-22 16:02:15.530][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-06-22 16:02:15.531][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:15.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:15.534][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:15.535][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-06-22 16:02:15.536][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-06-22 16:02:15.538][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-06-22 16:02:15.539][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:15.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:15.541][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:15.545][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-06-22 16:02:15.592][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-22 16:02:15.614][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-06-22 16:02:15.616][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-22 16:02:15.617][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-22 16:02:15.618][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-22 16:02:15.620][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-22 16:02:15.622][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-22 16:02:15.623][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-22 16:02:15.624][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-22 16:02:15.625][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-22 16:02:15.627][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-22 16:02:15.628][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-06-22 16:02:15.629][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-22 16:02:15.630][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:02:15.632][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-22 16:02:15.633][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-22 16:02:15.633][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-22 16:02:15.633][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-22 16:02:15.633][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-22 16:02:15.633][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-22 16:02:15.634][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-22 16:02:15.636][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-22 16:02:15.637][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-22 16:02:15.638][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-22 16:02:15.639][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-22 16:02:15.640][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-22 16:02:15.642][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-22 16:02:15.643][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:02:15.644][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-22 16:02:15.645][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-22 16:02:15.646][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-22 16:02:15.648][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:02:15.649][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-06-22 16:02:15.652][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-22 16:02:15.653][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-06-22 16:02:15.654][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-22 16:02:15.656][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-22 16:02:15.657][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-22 16:02:15.658][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-22 16:02:15.659][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-22 16:02:15.660][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-22 16:02:15.662][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-22 16:02:15.663][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-22 16:02:15.664][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-22 16:02:15.666][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-06-22 16:02:15.667][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-22 16:02:15.668][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:02:15.670][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-22 16:02:15.671][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-22 16:02:15.671][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-22 16:02:15.671][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-22 16:02:15.671][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-22 16:02:15.671][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-22 16:02:15.673][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-22 16:02:15.674][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-22 16:02:15.680][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-22 16:02:15.682][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-22 16:02:15.683][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-22 16:02:15.684][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-22 16:02:15.685][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-22 16:02:15.686][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:02:15.687][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-22 16:02:15.688][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-22 16:02:15.690][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-22 16:02:15.691][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:02:15.692][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-06-22 16:02:15.694][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-22 16:02:15.696][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-06-22 16:02:15.697][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-22 16:02:15.698][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-22 16:02:15.699][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-22 16:02:15.700][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-22 16:02:15.702][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-22 16:02:15.703][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-22 16:02:15.704][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-22 16:02:15.705][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-22 16:02:15.707][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-22 16:02:15.708][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-06-22 16:02:15.709][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-22 16:02:15.710][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:02:15.712][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-22 16:02:15.713][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:02:15.714][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-22 16:02:15.716][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-22 16:02:15.717][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-22 16:02:15.718][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-22 16:02:15.719][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-22 16:02:15.720][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-22 16:02:15.722][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-22 16:02:15.723][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:02:15.724][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-22 16:02:15.725][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-22 16:02:15.727][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-22 16:02:15.728][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:02:15.729][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-06-22 16:02:15.733][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-22 16:02:15.735][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-06-22 16:02:15.737][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-22 16:02:15.738][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-22 16:02:15.740][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-22 16:02:15.741][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-22 16:02:15.743][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-22 16:02:15.744][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-22 16:02:15.746][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-22 16:02:15.747][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-22 16:02:15.748][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-22 16:02:15.750][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-06-22 16:02:15.751][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-22 16:02:15.752][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:02:15.753][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-22 16:02:15.755][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:02:15.756][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-22 16:02:15.757][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-22 16:02:15.758][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-22 16:02:15.759][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-22 16:02:15.761][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-22 16:02:15.762][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-22 16:02:15.763][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-22 16:02:15.764][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:02:15.766][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-22 16:02:15.767][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-22 16:02:15.768][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-22 16:02:15.769][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:02:15.774][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-22 16:02:15.775][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:15.776][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[2024-06-22 16:02:15.777][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:15.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:15.779][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:15.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:15.782][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[2024-06-22 16:02:15.783][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:15.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:15.785][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:15.786][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:15.787][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:15.788][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:15.789][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:15.791][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:15.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:15.793][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:15.794][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:15.795][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:15.796][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:15.797][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:15.799][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:15.800][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:15.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:15.802][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:15.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:15.804][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:15.805][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:15.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:15.808][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:15.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:15.810][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:15.811][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:15.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:15.813][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:15.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:15.816][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:15.817][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:15.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:15.819][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:15.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:15.821][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:15.823][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:15.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:15.825][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:15.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:15.827][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:15.828][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:15.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:15.831][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:15.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:15.833][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:15.834][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:15.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:15.836][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:15.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:15.839][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:15.840][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:15.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:15.842][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:15.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:15.844][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[2024-06-22 16:02:15.846][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:15.847][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:15.848][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:15.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:15.850][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[2024-06-22 16:02:15.851][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:15.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:15.854][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:15.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:15.856][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[2024-06-22 16:02:15.858][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:15.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:15.860][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:15.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:15.862][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[2024-06-22 16:02:15.864][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:15.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:15.866][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:15.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:15.868][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:15.870][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:15.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:15.872][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:15.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:15.874][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:15.876][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-06-22 16:02:15.881][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-06-22 16:02:15.884][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-06-22 16:02:15.886][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-06-22 16:02:15.888][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-22 16:02:15.889][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-22 16:02:15.891][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-06-22 16:02:15.893][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-06-22 16:02:15.895][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-22 16:02:15.896][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-22 16:02:15.898][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-22 16:02:15.900][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-06-22 16:02:15.902][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-06-22 16:02:15.903][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-06-22 16:02:15.905][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-06-22 16:02:15.907][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-22 16:02:15.909][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-06-22 16:02:15.910][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-06-22 16:02:15.913][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-22 16:02:15.915][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-06-22 16:02:15.917][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-06-22 16:02:15.918][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-06-22 16:02:15.920][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-06-22 16:02:15.922][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-06-22 16:02:15.925][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-06-22 16:02:15.931][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-06-22 16:02:15.933][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-06-22 16:02:15.935][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-06-22 16:02:15.937][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-06-22 16:02:15.938][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-06-22 16:02:15.940][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-06-22 16:02:15.942][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-06-22 16:02:15.944][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-06-22 16:02:15.945][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-06-22 16:02:15.947][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-06-22 16:02:15.949][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-06-22 16:02:15.950][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-06-22 16:02:15.952][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-06-22 16:02:15.954][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-06-22 16:02:15.956][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-06-22 16:02:15.957][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-06-22 16:02:15.959][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-06-22 16:02:15.961][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-06-22 16:02:15.963][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-06-22 16:02:15.964][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-06-22 16:02:15.966][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-06-22 16:02:15.968][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-06-22 16:02:15.969][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-06-22 16:02:15.971][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-06-22 16:02:15.973][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-06-22 16:02:15.975][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-06-22 16:02:15.976][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-06-22 16:02:15.978][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-06-22 16:02:15.980][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-06-22 16:02:15.982][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-06-22 16:02:15.983][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-06-22 16:02:15.985][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-06-22 16:02:15.987][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-06-22 16:02:15.989][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-06-22 16:02:15.991][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-06-22 16:02:15.992][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-06-22 16:02:15.994][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-06-22 16:02:15.996][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-06-22 16:02:15.998][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-06-22 16:02:15.999][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-06-22 16:02:16.001][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-06-22 16:02:16.003][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-22 16:02:16.005][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-22 16:02:16.006][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-06-22 16:02:16.008][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-06-22 16:02:16.010][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-06-22 16:02:16.012][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-06-22 16:02:16.014][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-06-22 16:02:16.016][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-06-22 16:02:16.018][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-06-22 16:02:16.020][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-06-22 16:02:16.022][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-06-22 16:02:16.024][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-06-22 16:02:16.025][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-06-22 16:02:16.027][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-06-22 16:02:16.029][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-06-22 16:02:16.031][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-06-22 16:02:16.032][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-06-22 16:02:16.040][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-06-22 16:02:16.042][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-06-22 16:02:16.046][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-22 16:02:16.047][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:16.048][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:16.049][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:16.050][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:16.057][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:16.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:02:16.059][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:02:16.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:16.061][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:16.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:16.063][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:16.065][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:16.066][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:02:16.067][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:02:16.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:16.069][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:16.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:16.071][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:16.072][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:16.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:02:16.075][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:02:16.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:16.077][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:16.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:16.079][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:16.080][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:16.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:02:16.082][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:02:16.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:16.085][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:16.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:16.087][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:16.088][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:16.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:02:16.090][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:02:16.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:16.092][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:16.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:16.095][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:16.096][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:16.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:02:16.098][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:02:16.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:16.100][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:16.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:16.102][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:16.104][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:16.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:02:16.106][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:02:16.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:16.108][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:16.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:16.110][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:16.111][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:16.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:02:16.113][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:02:16.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:16.116][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:16.117][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:16.118][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:16.119][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:16.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:02:16.121][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:02:16.123][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:16.124][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:16.125][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:16.126][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:16.127][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:16.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:02:16.129][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:02:16.131][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:16.132][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:16.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:16.134][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:16.135][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:16.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:02:16.137][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:02:16.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:16.140][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:16.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:16.142][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:16.143][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:16.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:02:16.145][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:02:16.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:16.148][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:16.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:16.150][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:16.151][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:16.152][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:02:16.153][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:02:16.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:16.156][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:16.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:16.162][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:16.163][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:16.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:02:16.165][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:02:16.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:16.168][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:16.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:16.170][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:16.171][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:16.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:02:16.173][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:02:16.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:16.175][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:16.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:16.178][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:16.179][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:16.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:02:16.181][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:02:16.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:16.184][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:16.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:16.186][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:16.187][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:16.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:02:16.189][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:02:16.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:16.192][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:16.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:16.194][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:16.196][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.19-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/definitions.yml".
biodb.DEBUG[2024-06-22 16:02:16.210][self$getDbsInfo()$define] Define connector expasy.enzyme.
biodb.DEBUG[2024-06-22 16:02:16.213][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-22 16:02:16.214][self$setPropertyValue] Setting property "description" to "Write here the description of this database.".
biodb.DEBUG[2024-06-22 16:02:16.215][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-22 16:02:16.216][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-22 16:02:16.218][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-22 16:02:16.219][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-22 16:02:16.220][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-06-22 16:02:16.221][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-22 16:02:16.223][self$setPropertyValue] Setting property "entry.content.type" to "txt".
biodb.DEBUG[2024-06-22 16:02:16.224][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-22 16:02:16.225][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-22 16:02:16.226][self$setPropertyValue] Setting property "name" to "Expasy ENZYME database.".
biodb.DEBUG[2024-06-22 16:02:16.228][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-22 16:02:16.229][self$setPropertyValue] Setting property "parsing.expr" to "^ID\s+([0-9.]+)$".
biodb.DEBUG[2024-06-22 16:02:16.229][self$setPropertyValue] Setting property "parsing.expr" to "^CA\s+(.+?)\.?$".
biodb.DEBUG[2024-06-22 16:02:16.229][self$setPropertyValue] Setting property "parsing.expr" to "^CF\s+(.+?)\.?$".
biodb.DEBUG[2024-06-22 16:02:16.229][self$setPropertyValue] Setting property "parsing.expr" to "^DE\s+(.+?)\.?$".
biodb.DEBUG[2024-06-22 16:02:16.230][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-06-22 16:02:16.231][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-22 16:02:16.233][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-06-22 16:02:16.234][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-22 16:02:16.235][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-22 16:02:16.236][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-22 16:02:16.237][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-22 16:02:16.238][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-22 16:02:16.240][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-22 16:02:16.241][self$setPropertyValue] Setting property "urls" to "https://enzyme.expasy.org/".
biodb.DEBUG[2024-06-22 16:02:16.242][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-22 16:02:16.243][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-22 16:02:16.244][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-06-22 16:02:16.246][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:02:16.254][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-22 16:02:16.278][super$initialize] Initialize connector expasy.enzyme.
biodb.DEBUG[2024-06-22 16:02:16.280][super$initialize] Register connector expasy.enzyme with the request scheduler
biodb.DEBUG[2024-06-22 16:02:16.284][private$bdb$getRequestScheduler()$re ...] Register connector expasy.enzyme.
biodb.DEBUG[2024-06-22 16:02:16.289][private$addConnectorRules] Create new rule for URL "enzyme.expasy.org" of connector "expasy.enzyme".
biodb.DEBUG[2024-06-22 16:02:16.294][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-22 16:02:16.295][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-22 16:02:16.297][biodb$getFactory()$createConn] Creating new connector expasy.enzyme for database class expasy.enzyme .
biodb.INFO [2024-06-22 16:02:16.309][biodb::testThat]
biodb.INFO [2024-06-22 16:02:16.310][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-06-22 16:02:16.312][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-22 16:02:16.313][biodb::testThat]
biodb.TRACE[2024-06-22 16:02:16.317][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.19-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/testref/entry-expasy.enzyme-1.1.1.1-content.txt".
biodb.DEBUG[2024-06-22 16:02:16.319][biodb$getFactory()$createEntryFromCo ...] Creating Expasy ENZYME database. entries from 1 content(s).
biodb.DEBUG[2024-06-22 16:02:16.324][biodb$getFactory()$createEntryFromCo ...] Parsing 1 Expasy ENZYME database. entries.
biodb.DEBUG[2024-06-22 16:02:16.333][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-22 16:02:16.335][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:02:16.336][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:02:16.353][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:16.355][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:16.356][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:16.357][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-22 16:02:16.370][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:16.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:16.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:16.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:16.413][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-22 16:02:16.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-22 16:02:16.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:16.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:16.444][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-22 16:02:16.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-22 16:02:16.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:16.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:16.450][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:02:16.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:02:16.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:16.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:16.455][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-06-22 16:02:16.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-22 16:02:16.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:16.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:16.460][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-22 16:02:16.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-22 16:02:16.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:16.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:16.465][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-22 16:02:16.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-22 16:02:16.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:16.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:16.470][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-22 16:02:16.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-22 16:02:16.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:16.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:16.475][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-06-22 16:02:16.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-22 16:02:16.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:16.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:16.504][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:02:16.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:02:16.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:16.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:16.510][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:02:16.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:02:16.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:16.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:16.564][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:02:16.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:02:16.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:16.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:16.569][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:02:16.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:02:16.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:16.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:16.574][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:02:16.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:02:16.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:16.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:16.580][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:02:16.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:02:16.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:16.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:16.585][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:02:16.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:02:16.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:16.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:16.590][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:16.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:16.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:16.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:16.595][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:02:16.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:02:16.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:16.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:16.601][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:16.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:16.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:16.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:16.606][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:16.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:16.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:16.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:16.611][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:16.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:16.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:16.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:16.646][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:16.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:16.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:16.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:16.651][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:16.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:16.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:16.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:16.656][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:16.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:16.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:16.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-22 16:02:16.662][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 1.1.1.1.
biodb.TRACE[2024-06-22 16:02:16.665][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-22 16:02:16.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-22 16:02:16.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:16.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:16.670][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-22 16:02:16.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-22 16:02:16.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:16.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:16.675][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-22 16:02:16.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-22 16:02:16.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:16.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:16.680][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-22 16:02:16.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-22 16:02:16.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:16.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:16.703][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:16.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:16.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:16.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:16.725][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:02:16.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:02:16.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:16.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:16.736][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:16.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:16.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:16.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:16.741][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:16.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:16.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:16.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:16.747][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:16.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:16.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:16.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:16.754][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:16.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:16.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:16.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:16.759][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:16.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:16.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:16.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:16.765][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:16.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:16.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:16.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:16.770][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:02:16.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:02:16.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:16.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:16.776][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:02:16.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:02:16.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:16.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:16.781][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:02:16.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:02:16.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:16.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:16.796][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:16.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:16.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:16.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:16.802][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:16.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:16.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:16.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:16.807][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:16.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:16.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:16.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:16.812][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:16.814][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:16.815][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:16.816][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:16.817][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:16.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:16.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:16.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:16.835][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:02:16.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:02:16.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:16.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:16.840][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:02:16.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:02:16.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:16.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:16.845][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:02:16.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:02:16.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:16.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:16.850][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:02:16.856][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:02:16.858][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:16.859][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:16.860][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:02:16.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:02:16.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:16.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:16.875][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-22 16:02:16.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-22 16:02:16.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:16.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:16.880][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-22 16:02:16.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-22 16:02:16.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:16.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:16.885][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-22 16:02:16.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-22 16:02:16.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:16.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:16.890][ef$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-22 16:02:16.891][ef$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-22 16:02:16.892][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:16.893][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:16.895][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-22 16:02:16.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-22 16:02:16.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:16.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:16.910][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-22 16:02:16.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-22 16:02:16.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:16.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:16.915][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-22 16:02:16.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-22 16:02:16.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:16.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:16.920][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-22 16:02:16.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-22 16:02:16.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:16.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:16.925][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-22 16:02:16.926][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-22 16:02:16.927][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:16.929][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:16.930][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-22 16:02:16.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-22 16:02:16.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:16.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:16.945][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:16.947][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:16.948][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:16.949][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:16.956][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-22 16:02:16.957][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-22 16:02:16.958][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:16.960][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:16.966][ef$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-22 16:02:16.967][ef$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-22 16:02:16.969][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:16.970][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:16.976][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:02:16.978][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:02:16.979][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:16.980][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:17.004][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.19-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/testref/entry-expasy.enzyme-1.1.1.54-content.txt".
biodb.DEBUG[2024-06-22 16:02:17.059][biodb$getFactory()$createEntryFromCo ...] Creating Expasy ENZYME database. entries from 1 content(s).
biodb.DEBUG[2024-06-22 16:02:17.060][biodb$getFactory()$createEntryFromCo ...] Parsing 1 Expasy ENZYME database. entries.
biodb.DEBUG[2024-06-22 16:02:17.062][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-22 16:02:17.063][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:02:17.065][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:02:17.071][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:17.072][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:17.073][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:17.074][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-22 16:02:17.077][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:17.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:17.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:17.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:17.082][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-22 16:02:17.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-22 16:02:17.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:17.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:17.087][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:02:17.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:02:17.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:17.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:17.092][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-06-22 16:02:17.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-22 16:02:17.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:17.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:17.098][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:02:17.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:02:17.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:17.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:17.103][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:02:17.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:02:17.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:17.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:17.107][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:17.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:17.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:17.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:17.113][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:02:17.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:02:17.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:17.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:17.118][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:17.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:17.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:17.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:17.123][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:17.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:17.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:17.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:17.128][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:17.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:17.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:17.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:17.133][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:17.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:17.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:17.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:17.139][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:17.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:17.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:17.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:17.144][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:17.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:17.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:17.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-22 16:02:17.149][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 1.1.1.54.
biodb.TRACE[2024-06-22 16:02:17.177][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-22 16:02:17.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-22 16:02:17.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:17.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:17.182][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-22 16:02:17.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-22 16:02:17.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:17.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:17.187][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-22 16:02:17.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-22 16:02:17.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:17.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:17.192][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-22 16:02:17.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-22 16:02:17.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:17.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:17.198][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:17.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:17.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:17.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:17.208][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:02:17.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:02:17.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:17.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:17.218][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:17.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:17.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:17.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:17.223][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:17.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:17.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:17.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:17.228][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:17.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:17.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:17.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:17.235][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:17.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:17.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:17.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:17.244][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:17.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:17.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:17.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:17.249][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:17.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:17.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:17.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:17.254][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:02:17.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:02:17.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:17.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:17.259][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:02:17.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:02:17.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:17.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:17.264][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:02:17.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:02:17.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:17.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:17.290][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:17.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:17.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:17.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:17.295][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:17.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:17.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:17.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:17.300][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:17.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:17.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:17.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:17.305][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:17.307][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:17.308][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:17.309][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:17.310][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:17.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:17.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:17.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:17.325][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:02:17.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:02:17.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:17.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:17.330][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:02:17.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:02:17.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:17.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:17.335][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:02:17.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:02:17.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:17.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:17.340][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:02:17.341][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:02:17.342][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:17.343][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:17.344][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:02:17.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:02:17.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:17.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:17.359][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-22 16:02:17.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-22 16:02:17.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:17.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:17.364][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-22 16:02:17.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-22 16:02:17.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:17.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:17.369][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-22 16:02:17.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-22 16:02:17.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:17.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:17.374][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-22 16:02:17.375][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-22 16:02:17.377][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:17.378][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:17.379][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-22 16:02:17.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-22 16:02:17.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:17.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:17.394][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:17.395][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:17.396][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:17.397][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:17.404][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-22 16:02:17.405][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-22 16:02:17.406][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:17.407][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:17.414][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:02:17.416][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:02:17.417][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:17.418][ef$get] fields variable is a list.
biodb.INFO [2024-06-22 16:02:17.429][biodb::testThat]
biodb.INFO [2024-06-22 16:02:17.430][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-06-22 16:02:17.432][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-22 16:02:17.433][biodb::testThat]
biodb.DEBUG[2024-06-22 16:02:17.436][private$loadEntries] Creating entries from ids [2]: "1.1.1.1, 1.1.1.54".
biodb.DEBUG[2024-06-22 16:02:17.447][conn$getEntryContent] Get Expasy ENZYME database. entry content(s) for 2 id(s)...
biodb.TRACE[2024-06-22 16:02:17.455][cch$loadFileContent] Trying to load 2 files from cache: [2]: "1.1.1.1, 1.1.1.54".
biodb.INFO [2024-06-22 16:02:17.457][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280" for "expasy.enzyme-b59b84d962b6741050ba8f70ff4db280".
biodb.TRACE[2024-06-22 16:02:17.459][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2024-06-22 16:02:17.460][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-22 16:02:17.462][conn$getEntryContent] 0 Expasy ENZYME database. entry content(s) loaded from cache.
biodb.DEBUG[2024-06-22 16:02:17.463][conn$getEntryContent] 2 entry content(s) need to be fetched from Expasy ENZYME database. database "https://enzyme.expasy.org/".
biodb.DEBUG[2024-06-22 16:02:17.464][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-22 16:02:17.466][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-22 16:02:17.472][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-22 16:02:17.474][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:02:17.475][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:02:17.481][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:17.483][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:17.484][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:17.485][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:17.487][scheduler$sendRequest] Getting content of get URL request "https://enzyme.expasy.org/EC/1.1.1.1.txt".
biodb.DEBUG[2024-06-22 16:02:17.517][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-22 16:02:17.519][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-22 16:02:17.520][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/EC/1.1.1.1.txt".
biodb.TRACE[2024-06-22 16:02:18.209][getRCurlRequestResult] Using RCurl package for sending request (https://enzyme.expasy.org/EC/1.1.1.1.txt).
biodb.DEBUG[2024-06-22 16:02:18.653][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-22 16:02:18.655][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a52675cfd2f0c2b41556caa64d9341e3.content"
biodb.TRACE[2024-06-22 16:02:18.700][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a52675cfd2f0c2b41556caa64d9341e3.request"
biodb.DEBUG[2024-06-22 16:02:18.703][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-22 16:02:18.704][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:02:18.705][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:02:18.711][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:18.713][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:18.714][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:18.715][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:18.746][scheduler$sendRequest] Getting content of get URL request "https://enzyme.expasy.org/EC/1.1.1.54.txt".
biodb.DEBUG[2024-06-22 16:02:18.768][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-22 16:02:18.769][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-22 16:02:18.797][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/EC/1.1.1.54.txt".
biodb.TRACE[2024-06-22 16:02:19.129][getRCurlRequestResult] Using RCurl package for sending request (https://enzyme.expasy.org/EC/1.1.1.54.txt).
biodb.DEBUG[2024-06-22 16:02:19.569][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-22 16:02:19.572][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a9b93566a091cbe35a06e4b3871f95c9.content"
biodb.TRACE[2024-06-22 16:02:19.640][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a9b93566a091cbe35a06e4b3871f95c9.request"
biodb.TRACE[2024-06-22 16:02:19.643][private$doSaveContentToFile] Saving to cache [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/1.1.1.1.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/1.1.1.54.txt"
biodb.DEBUG[2024-06-22 16:02:19.647][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-22 16:02:19.649][self$createEntryFromContent] Creating Expasy ENZYME database. entries from 2 content(s).
biodb.DEBUG[2024-06-22 16:02:19.650][self$createEntryFromContent] Parsing 2 Expasy ENZYME database. entries.
biodb.DEBUG[2024-06-22 16:02:19.652][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-22 16:02:19.653][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:02:19.654][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:02:19.660][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:19.661][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:19.662][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:19.663][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-22 16:02:19.666][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:19.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:19.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:19.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:19.672][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-22 16:02:19.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-22 16:02:19.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:19.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:19.677][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:02:19.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:02:19.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:19.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:19.682][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-06-22 16:02:19.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-22 16:02:19.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:19.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:19.687][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:02:19.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:02:19.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:19.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:19.692][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:02:19.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:02:19.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:19.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:19.696][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:02:19.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:02:19.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:19.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:19.701][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:02:19.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:02:19.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:19.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:19.706][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:02:19.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:02:19.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:19.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:19.711][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:02:19.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:02:19.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:19.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:19.716][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:02:19.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:02:19.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:19.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:19.721][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:19.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:19.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:19.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:19.726][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:02:19.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:02:19.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:19.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:19.731][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:19.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:19.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:19.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:19.735][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:19.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:19.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:19.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:19.740][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:19.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:19.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:19.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-22 16:02:19.745][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-22 16:02:19.746][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:02:19.747][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:02:19.753][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:19.754][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:19.755][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:19.757][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-22 16:02:19.759][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:19.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:19.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:19.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:19.764][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-22 16:02:19.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-22 16:02:19.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:19.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:19.769][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:02:19.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:02:19.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:19.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:19.774][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-06-22 16:02:19.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-22 16:02:19.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:19.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:19.786][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:02:19.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:02:19.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:19.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:19.791][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:02:19.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:02:19.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:19.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:19.796][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:19.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:19.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:19.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:19.800][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:02:19.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-22 16:02:19.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:19.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:19.805][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:19.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:19.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:19.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:19.810][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:19.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:19.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:19.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:19.815][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:19.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:19.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:19.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:19.820][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:19.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:19.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:19.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:19.825][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:19.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:19.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:19.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:19.829][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:19.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:19.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:19.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:19.834][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:19.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:19.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:19.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:19.839][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:19.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:19.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:19.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:19.844][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-22 16:02:19.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-22 16:02:19.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:19.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-22 16:02:19.849][self$createEntryFromContent] Accession numbers: 1.1.1.1, 1.1.1.54.
biodb.TRACE[2024-06-22 16:02:19.850][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-06-22 16:02:19.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-06-22 16:02:19.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:19.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:19.855][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-06-22 16:02:19.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-06-22 16:02:19.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:19.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:19.860][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-06-22 16:02:19.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-06-22 16:02:19.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:19.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:19.870][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-06-22 16:02:19.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-06-22 16:02:19.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:19.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:19.875][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-06-22 16:02:19.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-06-22 16:02:19.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:19.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:19.880][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-06-22 16:02:19.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-06-22 16:02:19.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:19.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-22 16:02:19.894][biodb::testThat]
biodb.INFO [2024-06-22 16:02:19.895][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-06-22 16:02:19.896][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-22 16:02:19.898][biodb::testThat]
biodb.TRACE[2024-06-22 16:02:19.901][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:02:19.903][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:02:19.904][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:19.905][ef$get] fields variable is a list.
biodb.DEBUG[2024-06-22 16:02:19.906][function(conn, opt)] Testing searchForEntries() with entry "1.1.1.1" and field "name".
biodb.TRACE[2024-06-22 16:02:19.945][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:02:19.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:02:19.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:19.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:19.950][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:02:19.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:02:19.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:19.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:19.955][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:02:19.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:02:19.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:19.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-22 16:02:19.963][function(conn, opt)] With value "alcohol dehydrogenase".
biodb.DEBUG[2024-06-22 16:02:19.966][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://enzyme.expasy.org/enzyme-byname.html?alcohol dehydrogenase".
biodb.DEBUG[2024-06-22 16:02:19.969][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-22 16:02:19.970][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-22 16:02:19.972][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase".
biodb.TRACE[2024-06-22 16:02:20.442][getRCurlRequestResult] Using RCurl package for sending request (https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase).
biodb.DEBUG[2024-06-22 16:02:20.914][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-22 16:02:20.917][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.content"
biodb.TRACE[2024-06-22 16:02:20.923][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.request"
biodb.DEBUG[2024-06-22 16:02:20.930][function(conn, opt)] With found IDs [1]: "1.1.1.1".
biodb.INFO [2024-06-22 16:02:20.951][biodb::testThat]
biodb.INFO [2024-06-22 16:02:20.953][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-06-22 16:02:20.954][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-22 16:02:20.955][biodb::testThat]
biodb.TRACE[2024-06-22 16:02:20.989][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:02:20.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:02:20.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:20.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:20.994][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:02:20.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:02:20.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:20.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:20.999][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:02:21.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:02:21.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:21.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-22 16:02:21.048][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://enzyme.expasy.org/enzyme-byname.html?alcohol dehydrogenase".
biodb.DEBUG[2024-06-22 16:02:21.051][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-22 16:02:21.073][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f603fa2a57aec59588edc37541c6f6d5".
biodb.TRACE[2024-06-22 16:02:21.075][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-22 16:02:21.077][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.content".
biodb.INFO [2024-06-22 16:02:21.099][biodb::testThat]
biodb.INFO [2024-06-22 16:02:21.101][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-06-22 16:02:21.102][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-22 16:02:21.103][biodb::testThat]
biodb.TRACE[2024-06-22 16:02:21.115][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-22 16:02:21.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-22 16:02:21.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:21.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:21.121][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-22 16:02:21.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-22 16:02:21.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:21.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:21.125][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-22 16:02:21.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-22 16:02:21.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:21.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:21.130][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-22 16:02:21.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-22 16:02:21.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:21.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:21.185][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-22 16:02:21.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-22 16:02:21.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:21.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:21.191][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-22 16:02:21.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-22 16:02:21.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:21.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:21.196][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-22 16:02:21.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-22 16:02:21.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:21.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:21.201][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-22 16:02:21.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-22 16:02:21.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:21.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-22 16:02:21.216][biodb::testThat]
biodb.INFO [2024-06-22 16:02:21.217][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-06-22 16:02:21.218][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-22 16:02:21.219][biodb::testThat]
biodb.INFO [2024-06-22 16:02:21.231][biodb::testThat]
biodb.INFO [2024-06-22 16:02:21.232][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-06-22 16:02:21.234][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-22 16:02:21.235][biodb::testThat]
biodb.INFO [2024-06-22 16:02:21.245][biodb::testThat]
biodb.INFO [2024-06-22 16:02:21.246][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-06-22 16:02:21.248][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-22 16:02:21.249][biodb::testThat]
biodb.DEBUG[2024-06-22 16:02:21.268][function(conn, opt)] Trying to download "https://enzyme.expasy.org/cgi-bin/enzyme/enzyme-search-ec?field1=1&field2=1&field3=1&field4=1".
biodb.DEBUG[2024-06-22 16:02:21.727][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 [2024-06-22 16:02:22.203][biodb::testThat]
biodb.INFO [2024-06-22 16:02:22.204][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-06-22 16:02:22.205][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-22 16:02:22.207][biodb::testThat]
biodb.DEBUG[2024-06-22 16:02:22.666][getUrlContent] Use base::url() for downloading content of URL https://enzyme.expasy.org/images/1.1.1.1/image.png.
biodb.TRACE[2024-06-22 16:02:23.142][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:02:23.144][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:02:23.145][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:23.146][ef$get] fields variable is a list.
biodb.TRACE[2024-06-22 16:02:23.148][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-22 16:02:23.149][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-22 16:02:23.151][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-22 16:02:23.152][ef$get] fields variable is a list.
biodb.INFO [2024-06-22 16:02:23.153][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-06-22 16:02:23.164][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector expasy.enzyme from the request scheduler
biodb.INFO [2024-06-22 16:02:23.166][self$deleteConn] Connector "expasy.enzyme" deleted.
biodb.DEBUG[2024-06-22 16:02:23.167][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-06-22 16:02:23.168][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:02:23.169][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:02:23.170][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:23.171][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:23.172][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:23.173][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-06-22 16:02:23.186][biodb::testContext]
biodb.INFO [2024-06-22 16:02:23.187][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-22 16:02:23.189][biodb::testContext] Test context - Example long tests
biodb.INFO [2024-06-22 16:02:23.190][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-22 16:02:23.191][biodb::testContext]
biodb.INFO [2024-06-22 16:02:23.194][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-06-22 16:02:23.197][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-06-22 16:02:23.201][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-22 16:02:23.203][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-06-22 16:02:23.204][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-06-22 16:02:23.205][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:23.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:23.208][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:23.209][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-06-22 16:02:23.210][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-06-22 16:02:23.211][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:23.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:23.214][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:23.215][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-06-22 16:02:23.216][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-06-22 16:02:23.217][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:23.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:23.220][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:23.221][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-06-22 16:02:23.222][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-06-22 16:02:23.223][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-06-22 16:02:23.225][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:23.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:23.227][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:23.228][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-06-22 16:02:23.229][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-06-22 16:02:23.231][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-06-22 16:02:23.232][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:23.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:23.234][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:23.235][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-06-22 16:02:23.237][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-06-22 16:02:23.238][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:23.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:23.240][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:23.241][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-06-22 16:02:23.242][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-06-22 16:02:23.244][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-06-22 16:02:23.245][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:23.246][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:23.247][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:23.248][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-06-22 16:02:23.250][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-06-22 16:02:23.251][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:23.252][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:23.253][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:23.254][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-06-22 16:02:23.256][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-06-22 16:02:23.257][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-06-22 16:02:23.258][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:23.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:23.260][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:23.262][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-06-22 16:02:23.263][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-06-22 16:02:23.264][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-06-22 16:02:23.266][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-06-22 16:02:23.267][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-06-22 16:02:23.268][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-06-22 16:02:23.269][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:23.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:23.272][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:23.273][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-06-22 16:02:23.274][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-06-22 16:02:23.276][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:23.277][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:23.278][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:23.279][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-06-22 16:02:23.281][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-06-22 16:02:23.282][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:23.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:23.284][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:23.285][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-06-22 16:02:23.287][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-06-22 16:02:23.288][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:23.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:23.290][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:23.292][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-06-22 16:02:23.293][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-06-22 16:02:23.294][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:23.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:23.297][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:23.298][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-06-22 16:02:23.299][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-06-22 16:02:23.300][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:23.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:23.303][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:23.304][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-06-22 16:02:23.306][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-06-22 16:02:23.322][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-06-22 16:02:23.323][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:23.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:23.325][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:23.327][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-06-22 16:02:23.328][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-06-22 16:02:23.329][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-06-22 16:02:23.330][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:23.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:23.333][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:23.334][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-06-22 16:02:23.336][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-22 16:02:23.338][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-06-22 16:02:23.339][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-22 16:02:23.340][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-22 16:02:23.341][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-22 16:02:23.343][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-22 16:02:23.344][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-22 16:02:23.345][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-22 16:02:23.346][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-22 16:02:23.348][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-22 16:02:23.349][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-22 16:02:23.350][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-06-22 16:02:23.352][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-22 16:02:23.353][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:02:23.354][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-22 16:02:23.356][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-22 16:02:23.356][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-22 16:02:23.356][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-22 16:02:23.356][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-22 16:02:23.356][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-22 16:02:23.357][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-22 16:02:23.358][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-22 16:02:23.359][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-22 16:02:23.361][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-22 16:02:23.362][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-22 16:02:23.363][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-22 16:02:23.364][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-22 16:02:23.365][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:02:23.366][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-22 16:02:23.368][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-22 16:02:23.369][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-22 16:02:23.370][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:02:23.372][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-06-22 16:02:23.374][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-22 16:02:23.375][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-06-22 16:02:23.376][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-22 16:02:23.378][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-22 16:02:23.379][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-22 16:02:23.380][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-22 16:02:23.381][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-22 16:02:23.382][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-22 16:02:23.384][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-22 16:02:23.385][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-22 16:02:23.386][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-22 16:02:23.387][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-06-22 16:02:23.389][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-22 16:02:23.390][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:02:23.391][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-22 16:02:23.392][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-22 16:02:23.392][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-22 16:02:23.392][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-22 16:02:23.392][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-22 16:02:23.392][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-22 16:02:23.394][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-22 16:02:23.395][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-22 16:02:23.396][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-22 16:02:23.397][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-22 16:02:23.399][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-22 16:02:23.400][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-22 16:02:23.401][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-22 16:02:23.402][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:02:23.403][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-22 16:02:23.404][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-22 16:02:23.406][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-22 16:02:23.407][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:02:23.408][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-06-22 16:02:23.411][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-22 16:02:23.412][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-06-22 16:02:23.413][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-22 16:02:23.415][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-22 16:02:23.416][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-22 16:02:23.417][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-22 16:02:23.418][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-22 16:02:23.420][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-22 16:02:23.421][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-22 16:02:23.422][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-22 16:02:23.423][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-22 16:02:23.425][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-06-22 16:02:23.426][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-22 16:02:23.427][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:02:23.429][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-22 16:02:23.430][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:02:23.431][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-22 16:02:23.432][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-22 16:02:23.433][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-22 16:02:23.435][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-22 16:02:23.436][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-22 16:02:23.437][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-22 16:02:23.438][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-22 16:02:23.440][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:02:23.441][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-22 16:02:23.442][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-22 16:02:23.443][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-22 16:02:23.445][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:02:23.446][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-06-22 16:02:23.448][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-22 16:02:23.450][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-06-22 16:02:23.451][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-22 16:02:23.452][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-22 16:02:23.453][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-22 16:02:23.455][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-22 16:02:23.456][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-22 16:02:23.457][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-22 16:02:23.463][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-22 16:02:23.464][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-22 16:02:23.465][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-22 16:02:23.466][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-06-22 16:02:23.468][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-22 16:02:23.469][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:02:23.470][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-22 16:02:23.471][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:02:23.472][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-22 16:02:23.474][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-22 16:02:23.475][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-22 16:02:23.476][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-22 16:02:23.477][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-22 16:02:23.478][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-22 16:02:23.480][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-22 16:02:23.481][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:02:23.482][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-22 16:02:23.483][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-22 16:02:23.484][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-22 16:02:23.486][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:02:23.487][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-22 16:02:23.488][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:23.489][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:23.491][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:23.492][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:23.493][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:23.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:23.495][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:23.496][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:23.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:23.498][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:23.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:23.500][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:23.502][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:23.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:23.504][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:23.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:23.506][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:23.507][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:23.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:23.509][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:23.510][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:23.512][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:23.513][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:23.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:23.515][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:23.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:23.518][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:23.519][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:23.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:23.521][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:23.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:23.524][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:23.525][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:23.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:23.527][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:23.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:23.529][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:23.530][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:23.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:23.533][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:23.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:23.535][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:23.536][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:23.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:23.538][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:23.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:23.540][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:23.542][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:23.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:23.545][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:23.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:23.548][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:23.549][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:23.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:23.551][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:23.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:23.554][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:23.555][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:23.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:23.558][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:23.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:23.560][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:23.561][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:23.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:23.563][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:23.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:23.565][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:23.567][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:23.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:23.570][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:23.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:23.572][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:23.573][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:23.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:23.575][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:23.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:23.578][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:23.579][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:23.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:23.581][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:23.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:23.583][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:23.585][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:23.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:23.587][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:23.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:23.589][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:23.590][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-06-22 16:02:23.592][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-06-22 16:02:23.594][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-06-22 16:02:23.595][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-06-22 16:02:23.597][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-22 16:02:23.599][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-22 16:02:23.605][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-06-22 16:02:23.607][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-06-22 16:02:23.608][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-22 16:02:23.610][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-22 16:02:23.612][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-22 16:02:23.613][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-06-22 16:02:23.615][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-06-22 16:02:23.617][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-06-22 16:02:23.618][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-06-22 16:02:23.620][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-22 16:02:23.622][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-06-22 16:02:23.623][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-06-22 16:02:23.625][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-22 16:02:23.627][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-06-22 16:02:23.629][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-06-22 16:02:23.630][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-06-22 16:02:23.632][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-06-22 16:02:23.634][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-06-22 16:02:23.635][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-06-22 16:02:23.637][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-06-22 16:02:23.639][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-06-22 16:02:23.641][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-06-22 16:02:23.642][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-06-22 16:02:23.644][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-06-22 16:02:23.646][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-06-22 16:02:23.647][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-06-22 16:02:23.649][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-06-22 16:02:23.651][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-06-22 16:02:23.653][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-06-22 16:02:23.655][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-06-22 16:02:23.657][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-06-22 16:02:23.658][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-06-22 16:02:23.660][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-06-22 16:02:23.662][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-06-22 16:02:23.664][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-06-22 16:02:23.665][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-06-22 16:02:23.667][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-06-22 16:02:23.669][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-06-22 16:02:23.671][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-06-22 16:02:23.672][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-06-22 16:02:23.674][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-06-22 16:02:23.676][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-06-22 16:02:23.678][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-06-22 16:02:23.679][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-06-22 16:02:23.681][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-06-22 16:02:23.683][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-06-22 16:02:23.684][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-06-22 16:02:23.686][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-06-22 16:02:23.688][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-06-22 16:02:23.690][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-06-22 16:02:23.691][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-06-22 16:02:23.693][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-06-22 16:02:23.695][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-06-22 16:02:23.697][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-06-22 16:02:23.698][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-06-22 16:02:23.700][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-06-22 16:02:23.702][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-06-22 16:02:23.703][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-06-22 16:02:23.705][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-06-22 16:02:23.707][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-06-22 16:02:23.709][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-22 16:02:23.710][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-22 16:02:23.712][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-06-22 16:02:23.714][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-06-22 16:02:23.716][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-06-22 16:02:23.717][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-06-22 16:02:23.719][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-06-22 16:02:23.721][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-06-22 16:02:23.722][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-06-22 16:02:23.724][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-06-22 16:02:23.726][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-06-22 16:02:23.728][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-06-22 16:02:23.730][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-06-22 16:02:23.731][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-06-22 16:02:23.733][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-06-22 16:02:23.739][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-06-22 16:02:23.741][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-06-22 16:02:23.743][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-06-22 16:02:23.745][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-06-22 16:02:23.746][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-22 16:02:23.747][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:23.748][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:23.750][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:23.751][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:23.752][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:23.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:02:23.754][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:02:23.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:23.756][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:23.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:23.758][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[2024-06-22 16:02:23.759][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:23.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:02:23.762][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:02:23.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:23.764][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:23.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:23.766][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:23.767][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:23.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:02:23.769][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:02:23.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:23.771][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:23.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:23.774][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:23.775][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:23.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:02:23.777][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:02:23.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:23.779][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:23.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:23.781][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:23.783][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:23.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:02:23.785][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:02:23.786][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:23.787][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:23.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:23.789][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[2024-06-22 16:02:23.790][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:23.791][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:02:23.792][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:02:23.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:23.795][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:23.796][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:23.797][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:23.798][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:23.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:02:23.800][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:02:23.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:23.802][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:23.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:23.805][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:23.806][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:23.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:02:23.808][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:02:23.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:23.810][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:23.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:23.812][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:23.814][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:23.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:02:23.816][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:02:23.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:23.818][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:23.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:23.820][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:23.821][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:23.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:02:23.823][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:02:23.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:23.826][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:23.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:23.828][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:23.829][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:23.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:02:23.831][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:02:23.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:23.833][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:23.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:23.836][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:23.837][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:23.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:02:23.839][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:02:23.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:23.841][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:23.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:23.843][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:23.844][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:23.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:02:23.847][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:02:23.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:23.849][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:23.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:23.851][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:23.852][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:23.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:02:23.854][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:02:23.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:23.856][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:23.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:23.859][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:23.860][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:23.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:02:23.862][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:02:23.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:23.865][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:23.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:23.867][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:23.868][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:23.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:02:23.874][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:02:23.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:23.877][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:23.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:23.879][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:23.880][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-22 16:02:23.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:02:23.882][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:02:23.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:23.884][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:23.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:23.887][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-22 16:02:23.889][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.19-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/definitions.yml".
biodb.DEBUG[2024-06-22 16:02:23.891][self$getDbsInfo()$define] Define connector expasy.enzyme.
biodb.DEBUG[2024-06-22 16:02:23.893][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-22 16:02:23.894][self$setPropertyValue] Setting property "description" to "Write here the description of this database.".
biodb.DEBUG[2024-06-22 16:02:23.896][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-22 16:02:23.897][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-22 16:02:23.898][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-22 16:02:23.900][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-22 16:02:23.901][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-06-22 16:02:23.902][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-22 16:02:23.904][self$setPropertyValue] Setting property "entry.content.type" to "txt".
biodb.DEBUG[2024-06-22 16:02:23.906][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-22 16:02:23.907][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-22 16:02:23.908][self$setPropertyValue] Setting property "name" to "Expasy ENZYME database.".
biodb.DEBUG[2024-06-22 16:02:23.909][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-22 16:02:23.911][self$setPropertyValue] Setting property "parsing.expr" to "^ID\s+([0-9.]+)$".
biodb.DEBUG[2024-06-22 16:02:23.911][self$setPropertyValue] Setting property "parsing.expr" to "^CA\s+(.+?)\.?$".
biodb.DEBUG[2024-06-22 16:02:23.911][self$setPropertyValue] Setting property "parsing.expr" to "^CF\s+(.+?)\.?$".
biodb.DEBUG[2024-06-22 16:02:23.911][self$setPropertyValue] Setting property "parsing.expr" to "^DE\s+(.+?)\.?$".
biodb.DEBUG[2024-06-22 16:02:23.912][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-06-22 16:02:23.913][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-22 16:02:23.915][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-06-22 16:02:23.916][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-22 16:02:23.917][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-22 16:02:23.918][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-22 16:02:23.919][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-22 16:02:23.920][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-22 16:02:23.922][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-22 16:02:23.923][self$setPropertyValue] Setting property "urls" to "https://enzyme.expasy.org/".
biodb.DEBUG[2024-06-22 16:02:23.924][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-22 16:02:23.925][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-22 16:02:23.926][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-06-22 16:02:23.928][self$setPropertyValue]
biodb.DEBUG[2024-06-22 16:02:23.929][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-22 16:02:23.934][super$initialize] Initialize connector expasy.enzyme.
biodb.DEBUG[2024-06-22 16:02:23.935][super$initialize] Register connector expasy.enzyme with the request scheduler
biodb.DEBUG[2024-06-22 16:02:23.936][private$bdb$getRequestScheduler()$re ...] Register connector expasy.enzyme.
biodb.DEBUG[2024-06-22 16:02:23.938][private$addConnectorRules] Create new rule for URL "enzyme.expasy.org" of connector "expasy.enzyme".
biodb.DEBUG[2024-06-22 16:02:23.940][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-22 16:02:23.941][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-22 16:02:23.942][biodb$getFactory()$createConn] Creating new connector expasy.enzyme for database class expasy.enzyme .
biodb.INFO [2024-06-22 16:02:23.943][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-06-22 16:02:23.945][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector expasy.enzyme from the request scheduler
biodb.INFO [2024-06-22 16:02:23.946][self$deleteConn] Connector "expasy.enzyme" deleted.
biodb.DEBUG[2024-06-22 16:02:23.947][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-06-22 16:02:23.948][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-22 16:02:23.949][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-22 16:02:23.950][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-22 16:02:23.952][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-22 16:02:23.953][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-06-22 16:02:23.954][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 85 ]

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

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 85 ]
Error: Test failures
Execution halted

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/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 ‘/Users/biocbuild/bbs-3.19-bioc-longtests/meat/biodbExpasy.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.4
* 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 dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... SKIPPED
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘longtests/testthat.R’ failed.
Last 13 lines of output:
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_long_100_generic.R:37:1'): The entry image URL can be downloaded. ──
  Error in `charToRaw(content)`: argument must be a character vector of length 1
  Backtrace:
      ▆
   1. ├─base::do.call(fct, params)
   2. └─biodb (local) `<fn>`(conn = `<ExpsyEnC>`, opt = `<named list>`)
   3.   └─biodb:::getUrlContent(url, binary = TRUE)
   4.     └─biodb:::getBaseUrlContent(u, binary = binary)
   5.       └─base::charToRaw(content)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 85 ]
  Error: Test failures
  Execution halted
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/Users/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)