Back to Long Tests report for BioC 3.20

This page was generated on 2024-09-07 23:55 -0400 (Sat, 07 Sep 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4711
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4448
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4481
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 7/32HostnameOS / ArchCHECK
biodbExpasy 1.9.0  (landing page)
Pierrick Roger
Snapshot Date: 2024-09-07 09:55 -0400 (Sat, 07 Sep 2024)
git_url: https://git.bioconductor.org/packages/biodbExpasy
git_branch: devel
git_last_commit: 25fc0fc
git_last_commit_date: 2024-04-30 11:41:12 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  ERROR  
palomino8Windows Server 2022 Datacenter / x64  ERROR  
lconwaymacOS 12.7.1 Monterey / x86_64  ERROR  

CHECK results for biodbExpasy on palomino8

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

raw results


Summary

Package: biodbExpasy
Version: 1.9.0
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbExpasy_1.9.0.tar.gz
StartedAt: 2024-09-07 16:02:47 -0400 (Sat, 07 Sep 2024)
EndedAt: 2024-09-07 16:03:39 -0400 (Sat, 07 Sep 2024)
EllapsedTime: 52.1 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbExpasy.Rcheck
Warnings: NA

Tests output

biodbExpasy.Rcheck/tests/testthat.Rout.fail


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

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> # 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 [2024-09-07 16:03:31.089][biodb::testContext]
biodb.INFO [2024-09-07 16:03:31.093][biodb::testContext] ********************************************************************************
biodb.INFO [2024-09-07 16:03:31.094][biodb::testContext] Test context - Generic long tests
biodb.INFO [2024-09-07 16:03:31.096][biodb::testContext] ********************************************************************************
biodb.INFO [2024-09-07 16:03:31.097][biodb::testContext]
biodb.INFO [2024-09-07 16:03:31.105][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.13.0.
biodb.DEBUG[2024-09-07 16:03:31.108][self$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.20-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2024-09-07 16:03:31.140][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-09-07 16:03:31.142][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-09-07 16:03:31.144][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-09-07 16:03:31.145][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:31.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:31.148][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-07 16:03:31.149][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-09-07 16:03:31.180][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-09-07 16:03:31.181][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:31.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:31.184][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-07 16:03:31.185][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-09-07 16:03:31.186][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-09-07 16:03:31.187][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:31.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:31.189][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-07 16:03:31.191][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-09-07 16:03:31.192][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-09-07 16:03:31.193][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-09-07 16:03:31.194][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:31.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:31.196][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-07 16:03:31.198][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-09-07 16:03:31.199][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-09-07 16:03:31.200][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-09-07 16:03:31.201][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:31.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:31.203][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-07 16:03:31.205][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-09-07 16:03:31.206][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-09-07 16:03:31.207][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:31.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:31.209][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-07 16:03:31.210][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-09-07 16:03:31.212][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-09-07 16:03:31.213][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-09-07 16:03:31.214][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:31.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:31.216][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-07 16:03:31.217][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-09-07 16:03:31.219][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-09-07 16:03:31.220][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:31.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:31.222][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-07 16:03:31.223][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-09-07 16:03:31.224][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-09-07 16:03:31.226][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-09-07 16:03:31.227][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:31.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:31.229][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-07 16:03:31.230][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-09-07 16:03:31.231][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-09-07 16:03:31.233][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-09-07 16:03:31.234][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-09-07 16:03:31.235][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-09-07 16:03:31.236][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-09-07 16:03:31.237][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:31.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:31.240][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[2024-09-07 16:03:31.241][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-09-07 16:03:31.242][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-09-07 16:03:31.243][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:31.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:31.245][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-07 16:03:31.246][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-09-07 16:03:31.248][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-09-07 16:03:31.249][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:31.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:31.251][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-07 16:03:31.252][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-09-07 16:03:31.253][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-09-07 16:03:31.255][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:31.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:31.257][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-07 16:03:31.258][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-09-07 16:03:31.259][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-09-07 16:03:31.260][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:31.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:31.262][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-07 16:03:31.264][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-09-07 16:03:31.265][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-09-07 16:03:31.266][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:31.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:31.268][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-07 16:03:31.269][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-09-07 16:03:31.270][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-09-07 16:03:31.274][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-09-07 16:03:31.275][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:31.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:31.277][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-07 16:03:31.278][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-09-07 16:03:31.280][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-09-07 16:03:31.281][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-09-07 16:03:31.282][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:31.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:31.284][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-07 16:03:31.287][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-09-07 16:03:31.314][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-09-07 16:03:31.328][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-09-07 16:03:31.329][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-09-07 16:03:31.330][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-09-07 16:03:31.332][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-09-07 16:03:31.333][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-09-07 16:03:31.334][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-09-07 16:03:31.335][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-09-07 16:03:31.336][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-09-07 16:03:31.338][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-09-07 16:03:31.339][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-09-07 16:03:31.340][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-09-07 16:03:31.341][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-09-07 16:03:31.342][self$setPropertyValue]
biodb.DEBUG[2024-09-07 16:03:31.344][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-09-07 16:03:31.345][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-09-07 16:03:31.345][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-09-07 16:03:31.345][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-09-07 16:03:31.345][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-09-07 16:03:31.345][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-09-07 16:03:31.346][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-09-07 16:03:31.347][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-07 16:03:31.349][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-07 16:03:31.350][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-09-07 16:03:31.351][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-07 16:03:31.352][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-07 16:03:31.354][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-09-07 16:03:31.355][self$setPropertyValue]
biodb.DEBUG[2024-09-07 16:03:31.361][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-09-07 16:03:31.362][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-09-07 16:03:31.364][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-09-07 16:03:31.365][self$setPropertyValue]
biodb.DEBUG[2024-09-07 16:03:31.366][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-09-07 16:03:31.368][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-09-07 16:03:31.369][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-09-07 16:03:31.370][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-09-07 16:03:31.372][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-09-07 16:03:31.373][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-09-07 16:03:31.374][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-09-07 16:03:31.375][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-09-07 16:03:31.376][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-09-07 16:03:31.378][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-09-07 16:03:31.379][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-09-07 16:03:31.380][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-09-07 16:03:31.381][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-09-07 16:03:31.382][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-09-07 16:03:31.384][self$setPropertyValue]
biodb.DEBUG[2024-09-07 16:03:31.385][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-09-07 16:03:31.386][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-09-07 16:03:31.386][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-09-07 16:03:31.386][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-09-07 16:03:31.386][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-09-07 16:03:31.386][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-09-07 16:03:31.387][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-09-07 16:03:31.388][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-07 16:03:31.389][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-07 16:03:31.391][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-09-07 16:03:31.392][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-07 16:03:31.393][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-07 16:03:31.394][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-09-07 16:03:31.395][self$setPropertyValue]
biodb.DEBUG[2024-09-07 16:03:31.396][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-09-07 16:03:31.397][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-09-07 16:03:31.399][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-09-07 16:03:31.400][self$setPropertyValue]
biodb.DEBUG[2024-09-07 16:03:31.401][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-09-07 16:03:31.403][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-09-07 16:03:31.404][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-09-07 16:03:31.406][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-09-07 16:03:31.407][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-09-07 16:03:31.408][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-09-07 16:03:31.409][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-09-07 16:03:31.410][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-09-07 16:03:31.412][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-09-07 16:03:31.413][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-09-07 16:03:31.414][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-09-07 16:03:31.415][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-09-07 16:03:31.416][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-09-07 16:03:31.418][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-09-07 16:03:31.419][self$setPropertyValue]
biodb.DEBUG[2024-09-07 16:03:31.420][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-09-07 16:03:31.421][self$setPropertyValue]
biodb.DEBUG[2024-09-07 16:03:31.422][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-09-07 16:03:31.424][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-07 16:03:31.425][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-07 16:03:31.426][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-09-07 16:03:31.427][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-07 16:03:31.428][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-07 16:03:31.429][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-09-07 16:03:31.430][self$setPropertyValue]
biodb.DEBUG[2024-09-07 16:03:31.432][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-09-07 16:03:31.433][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-09-07 16:03:31.434][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-09-07 16:03:31.435][self$setPropertyValue]
biodb.DEBUG[2024-09-07 16:03:31.437][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-09-07 16:03:31.438][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-09-07 16:03:31.440][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-09-07 16:03:31.441][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-09-07 16:03:31.442][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-09-07 16:03:31.443][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-09-07 16:03:31.445][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-09-07 16:03:31.446][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-09-07 16:03:31.447][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-09-07 16:03:31.448][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-09-07 16:03:31.449][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-09-07 16:03:31.451][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-09-07 16:03:31.452][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-09-07 16:03:31.453][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-09-07 16:03:31.454][self$setPropertyValue]
biodb.DEBUG[2024-09-07 16:03:31.455][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-09-07 16:03:31.457][self$setPropertyValue]
biodb.DEBUG[2024-09-07 16:03:31.458][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-09-07 16:03:31.459][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-07 16:03:31.460][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-07 16:03:31.461][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-09-07 16:03:31.462][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-07 16:03:31.463][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-07 16:03:31.465][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-09-07 16:03:31.466][self$setPropertyValue]
biodb.DEBUG[2024-09-07 16:03:31.467][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-09-07 16:03:31.468][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-09-07 16:03:31.469][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-09-07 16:03:31.470][self$setPropertyValue]
biodb.DEBUG[2024-09-07 16:03:31.474][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-09-07 16:03:31.475][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:31.476][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[2024-09-07 16:03:31.477][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:31.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-07 16:03:31.479][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-07 16:03:31.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:31.482][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-07 16:03:31.483][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:31.484][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-07 16:03:31.485][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-07 16:03:31.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:31.487][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[2024-09-07 16:03:31.488][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:31.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-07 16:03:31.490][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-07 16:03:31.492][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:31.493][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[2024-09-07 16:03:31.495][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:31.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-07 16:03:31.497][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-07 16:03:31.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:31.499][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[2024-09-07 16:03:31.500][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:31.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-07 16:03:31.502][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-07 16:03:31.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:31.504][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-07 16:03:31.506][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:31.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-07 16:03:31.508][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-07 16:03:31.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:31.510][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-07 16:03:31.511][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:31.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-07 16:03:31.513][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-07 16:03:31.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:31.515][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-07 16:03:31.517][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:31.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-07 16:03:31.519][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-07 16:03:31.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:31.521][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-07 16:03:31.522][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:31.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-07 16:03:31.524][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-07 16:03:31.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:31.526][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-07 16:03:31.527][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:31.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-07 16:03:31.530][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-07 16:03:31.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:31.532][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-07 16:03:31.533][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:31.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-07 16:03:31.535][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-07 16:03:31.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:31.537][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-07 16:03:31.538][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:31.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-07 16:03:31.540][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-07 16:03:31.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:31.543][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-07 16:03:31.544][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:31.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-07 16:03:31.546][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-07 16:03:31.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:31.548][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[2024-09-07 16:03:31.549][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:31.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-07 16:03:31.551][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-07 16:03:31.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:31.554][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[2024-09-07 16:03:31.555][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:31.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-07 16:03:31.557][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-07 16:03:31.558][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:31.559][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-07 16:03:31.560][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:31.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-07 16:03:31.562][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-07 16:03:31.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:31.564][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-07 16:03:31.565][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:31.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-07 16:03:31.568][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-07 16:03:31.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:31.570][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-07 16:03:31.571][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-09-07 16:03:31.581][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-09-07 16:03:31.582][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-09-07 16:03:31.584][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-09-07 16:03:31.585][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-09-07 16:03:31.587][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-09-07 16:03:31.588][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-09-07 16:03:31.590][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-09-07 16:03:31.592][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-09-07 16:03:31.593][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-09-07 16:03:31.595][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-09-07 16:03:31.596][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-09-07 16:03:31.598][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-09-07 16:03:31.599][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-09-07 16:03:31.601][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-09-07 16:03:31.602][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-09-07 16:03:31.604][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-09-07 16:03:31.606][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-09-07 16:03:31.607][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-09-07 16:03:31.609][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-09-07 16:03:31.610][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-09-07 16:03:31.612][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-09-07 16:03:31.614][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-09-07 16:03:31.615][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-09-07 16:03:31.617][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-09-07 16:03:31.618][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-09-07 16:03:31.620][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-09-07 16:03:31.622][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-09-07 16:03:31.623][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-09-07 16:03:31.625][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-09-07 16:03:31.626][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-09-07 16:03:31.628][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-09-07 16:03:31.629][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-09-07 16:03:31.631][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-09-07 16:03:31.632][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-09-07 16:03:31.634][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-09-07 16:03:31.636][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-09-07 16:03:31.637][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-09-07 16:03:31.639][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-09-07 16:03:31.640][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-09-07 16:03:31.642][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-09-07 16:03:31.644][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-09-07 16:03:31.645][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-09-07 16:03:31.647][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-09-07 16:03:31.648][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-09-07 16:03:31.650][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-09-07 16:03:31.652][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-09-07 16:03:31.653][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-09-07 16:03:31.655][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-09-07 16:03:31.656][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-09-07 16:03:31.658][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-09-07 16:03:31.659][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-09-07 16:03:31.661][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-09-07 16:03:31.663][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-09-07 16:03:31.664][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-09-07 16:03:31.666][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-09-07 16:03:31.667][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-09-07 16:03:31.669][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-09-07 16:03:31.670][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-09-07 16:03:31.672][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-09-07 16:03:31.674][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-09-07 16:03:31.675][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-09-07 16:03:31.677][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-09-07 16:03:31.678][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-09-07 16:03:31.680][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-09-07 16:03:31.681][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-09-07 16:03:31.683][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-09-07 16:03:31.685][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-09-07 16:03:31.686][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-09-07 16:03:31.688][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-09-07 16:03:31.689][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-09-07 16:03:31.691][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-09-07 16:03:31.692][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-09-07 16:03:31.694][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-09-07 16:03:31.695][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-09-07 16:03:31.697][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-09-07 16:03:31.699][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-09-07 16:03:31.700][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-09-07 16:03:31.702][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-09-07 16:03:31.703][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-09-07 16:03:31.705][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-09-07 16:03:31.706][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-09-07 16:03:31.708][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-09-07 16:03:31.750][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-09-07 16:03:31.753][initialize] This is biodb version 1.13.0.
biodb.DEBUG[2024-09-07 16:03:31.755][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-09-07 16:03:31.757][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-09-07 16:03:31.758][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-07 16:03:31.759][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:31.760][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-07 16:03:31.764][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:31.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-07 16:03:31.767][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-07 16:03:31.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-07 16:03:31.769][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-07 16:03:31.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:31.771][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-07 16:03:31.772][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:31.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-07 16:03:31.774][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-07 16:03:31.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-07 16:03:31.776][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-07 16:03:31.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:31.779][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-07 16:03:31.780][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:31.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-07 16:03:31.782][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-07 16:03:31.783][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-07 16:03:31.784][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-07 16:03:31.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:31.786][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-07 16:03:31.787][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:31.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-07 16:03:31.789][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-07 16:03:31.791][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-07 16:03:31.792][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-07 16:03:31.793][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:31.794][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-07 16:03:31.795][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:31.796][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-07 16:03:31.797][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-07 16:03:31.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-07 16:03:31.799][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-07 16:03:31.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:31.802][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-07 16:03:31.803][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:31.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-07 16:03:31.805][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-07 16:03:31.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-07 16:03:31.813][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-07 16:03:31.814][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:31.815][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-07 16:03:31.816][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:31.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-07 16:03:31.818][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-07 16:03:31.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-07 16:03:31.820][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-07 16:03:31.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:31.822][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-07 16:03:31.824][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:31.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-07 16:03:31.826][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-07 16:03:31.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-07 16:03:31.828][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-07 16:03:31.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:31.830][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-07 16:03:31.831][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:31.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-07 16:03:31.833][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-07 16:03:31.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-07 16:03:31.836][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-07 16:03:31.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:31.838][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-07 16:03:31.839][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:31.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-07 16:03:31.841][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-07 16:03:31.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-07 16:03:31.843][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-07 16:03:31.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:31.845][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-07 16:03:31.846][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:31.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-07 16:03:31.849][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-07 16:03:31.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-07 16:03:31.851][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-07 16:03:31.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:31.853][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-07 16:03:31.854][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:31.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-07 16:03:31.856][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-07 16:03:31.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-07 16:03:31.859][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-07 16:03:31.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:31.861][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-07 16:03:31.862][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:31.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-07 16:03:31.864][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-07 16:03:31.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-07 16:03:31.866][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-07 16:03:31.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:31.869][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-07 16:03:31.870][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:31.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-07 16:03:31.872][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-07 16:03:31.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-07 16:03:31.874][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-07 16:03:31.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:31.876][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-07 16:03:31.877][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:31.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-07 16:03:31.880][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-07 16:03:31.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-07 16:03:31.882][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-07 16:03:31.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:31.884][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-07 16:03:31.885][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:31.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-07 16:03:31.887][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-07 16:03:31.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-07 16:03:31.890][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-07 16:03:31.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:31.892][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-07 16:03:31.893][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:31.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-07 16:03:31.895][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-07 16:03:31.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-07 16:03:31.897][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-07 16:03:31.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:31.899][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-07 16:03:31.903][biodb$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/definitions.yml".
biodb.DEBUG[2024-09-07 16:03:31.912][self$getDbsInfo()$define] Define connector expasy.enzyme.
biodb.DEBUG[2024-09-07 16:03:31.914][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-09-07 16:03:31.915][self$setPropertyValue] Setting property "description" to "Write here the description of this database.".
biodb.DEBUG[2024-09-07 16:03:31.917][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-09-07 16:03:31.918][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-09-07 16:03:31.919][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-09-07 16:03:31.920][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-09-07 16:03:31.921][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-09-07 16:03:31.923][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-09-07 16:03:31.924][self$setPropertyValue] Setting property "entry.content.type" to "txt".
biodb.DEBUG[2024-09-07 16:03:31.925][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-09-07 16:03:31.926][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-09-07 16:03:31.928][self$setPropertyValue] Setting property "name" to "Expasy ENZYME database.".
biodb.DEBUG[2024-09-07 16:03:31.929][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-09-07 16:03:31.930][self$setPropertyValue] Setting property "parsing.expr" to "^ID\s+([0-9.]+)$".
biodb.DEBUG[2024-09-07 16:03:31.930][self$setPropertyValue] Setting property "parsing.expr" to "^CA\s+(.+?)\.?$".
biodb.DEBUG[2024-09-07 16:03:31.930][self$setPropertyValue] Setting property "parsing.expr" to "^CF\s+(.+?)\.?$".
biodb.DEBUG[2024-09-07 16:03:31.930][self$setPropertyValue] Setting property "parsing.expr" to "^DE\s+(.+?)\.?$".
biodb.DEBUG[2024-09-07 16:03:31.931][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-09-07 16:03:31.933][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-09-07 16:03:31.934][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-09-07 16:03:31.935][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-07 16:03:31.936][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-07 16:03:31.937][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-09-07 16:03:31.938][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-07 16:03:31.939][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-07 16:03:31.941][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-09-07 16:03:31.942][self$setPropertyValue] Setting property "urls" to "https://enzyme.expasy.org/".
biodb.DEBUG[2024-09-07 16:03:31.943][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-09-07 16:03:31.944][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-09-07 16:03:31.945][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-09-07 16:03:31.946][self$setPropertyValue]
biodb.DEBUG[2024-09-07 16:03:31.952][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-09-07 16:03:31.975][super$initialize] Initialize connector expasy.enzyme.
biodb.DEBUG[2024-09-07 16:03:31.976][super$initialize] Register connector expasy.enzyme with the request scheduler
biodb.DEBUG[2024-09-07 16:03:31.980][private$bdb$getRequestScheduler()$re ...] Register connector expasy.enzyme.
biodb.DEBUG[2024-09-07 16:03:31.983][private$addConnectorRules] Create new rule for URL "enzyme.expasy.org" of connector "expasy.enzyme".
biodb.DEBUG[2024-09-07 16:03:31.987][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-09-07 16:03:31.988][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-09-07 16:03:31.990][biodb$getFactory()$createConn] Creating new connector expasy.enzyme for database class expasy.enzyme .
biodb.INFO [2024-09-07 16:03:32.000][biodb::testThat]
biodb.INFO [2024-09-07 16:03:32.001][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-09-07 16:03:32.003][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-07 16:03:32.004][biodb::testThat]
biodb.TRACE[2024-09-07 16:03:32.009][loadFileContents] Loaded 1 files from cache: [1]: "F:/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/testref/entry-expasy.enzyme-1.1.1.1-content.txt".
biodb.DEBUG[2024-09-07 16:03:32.011][biodb$getFactory()$createEntryFromCo ...] Creating Expasy ENZYME database. entries from 1 content(s).
biodb.DEBUG[2024-09-07 16:03:32.014][biodb$getFactory()$createEntryFromCo ...] Parsing 1 Expasy ENZYME database. entries.
biodb.DEBUG[2024-09-07 16:03:32.033][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-07 16:03:32.034][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-07 16:03:32.044][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-07 16:03:32.079][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-07 16:03:32.081][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-07 16:03:32.082][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:32.083][FUN] Functions in observer BiodbConfig: [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[2024-09-07 16:03:32.092][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-07 16:03:32.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-07 16:03:32.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.119][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-09-07 16:03:32.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-09-07 16:03:32.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.134][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-09-07 16:03:32.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-09-07 16:03:32.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.139][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-07 16:03:32.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-07 16:03:32.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.144][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-09-07 16:03:32.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-09-07 16:03:32.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.149][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-09-07 16:03:32.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-09-07 16:03:32.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.154][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-09-07 16:03:32.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-09-07 16:03:32.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.159][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-09-07 16:03:32.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-09-07 16:03:32.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.164][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-09-07 16:03:32.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-09-07 16:03:32.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.183][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-07 16:03:32.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-07 16:03:32.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.188][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-07 16:03:32.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-07 16:03:32.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.255][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-07 16:03:32.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-07 16:03:32.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.260][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-07 16:03:32.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-07 16:03:32.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.265][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-07 16:03:32.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-07 16:03:32.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.270][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-09-07 16:03:32.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-09-07 16:03:32.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.275][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-09-07 16:03:32.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-09-07 16:03:32.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.280][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-07 16:03:32.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-07 16:03:32.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.285][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-09-07 16:03:32.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-09-07 16:03:32.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.290][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-07 16:03:32.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-07 16:03:32.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.294][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-07 16:03:32.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-07 16:03:32.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.299][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-07 16:03:32.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-07 16:03:32.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.304][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-07 16:03:32.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-07 16:03:32.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.309][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-07 16:03:32.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-07 16:03:32.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.314][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-07 16:03:32.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-07 16:03:32.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-07 16:03:32.319][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 1.1.1.1.
biodb.TRACE[2024-09-07 16:03:32.322][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-09-07 16:03:32.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-09-07 16:03:32.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.327][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-09-07 16:03:32.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-09-07 16:03:32.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.332][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-09-07 16:03:32.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-09-07 16:03:32.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.337][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-09-07 16:03:32.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-09-07 16:03:32.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.363][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-07 16:03:32.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-07 16:03:32.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.382][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-09-07 16:03:32.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-09-07 16:03:32.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.393][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-07 16:03:32.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-07 16:03:32.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.398][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-07 16:03:32.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-07 16:03:32.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.409][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-07 16:03:32.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-07 16:03:32.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.415][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-07 16:03:32.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-07 16:03:32.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.420][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-07 16:03:32.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-07 16:03:32.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.425][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-07 16:03:32.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-07 16:03:32.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.430][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-09-07 16:03:32.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-09-07 16:03:32.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.435][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-09-07 16:03:32.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-09-07 16:03:32.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.440][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-09-07 16:03:32.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-09-07 16:03:32.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.455][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-07 16:03:32.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-07 16:03:32.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.460][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-07 16:03:32.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-07 16:03:32.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.465][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-07 16:03:32.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-07 16:03:32.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.470][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-07 16:03:32.471][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-07 16:03:32.472][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.473][ef$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.475][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-07 16:03:32.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-07 16:03:32.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.490][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-07 16:03:32.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-07 16:03:32.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.498][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-07 16:03:32.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-07 16:03:32.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.505][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-07 16:03:32.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-07 16:03:32.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.510][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-07 16:03:32.511][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-07 16:03:32.513][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.514][ef$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.515][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-07 16:03:32.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-07 16:03:32.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.530][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-09-07 16:03:32.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-09-07 16:03:32.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.535][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-09-07 16:03:32.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-09-07 16:03:32.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.540][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-09-07 16:03:32.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-09-07 16:03:32.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.545][ef$get] Asked field names are: cofactor.
biodb.TRACE[2024-09-07 16:03:32.546][ef$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-09-07 16:03:32.548][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.549][ef$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.550][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-09-07 16:03:32.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-09-07 16:03:32.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.565][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-09-07 16:03:32.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-09-07 16:03:32.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.570][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-09-07 16:03:32.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-09-07 16:03:32.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.575][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-09-07 16:03:32.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-09-07 16:03:32.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.580][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-09-07 16:03:32.581][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-09-07 16:03:32.583][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.584][ef$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.585][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-09-07 16:03:32.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-09-07 16:03:32.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.606][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-07 16:03:32.607][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-07 16:03:32.608][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.609][ef$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.616][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-09-07 16:03:32.618][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-09-07 16:03:32.619][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.620][ef$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.627][ef$get] Asked field names are: cofactor.
biodb.TRACE[2024-09-07 16:03:32.629][ef$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-09-07 16:03:32.630][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.631][ef$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.638][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-07 16:03:32.639][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-07 16:03:32.641][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.642][ef$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.660][loadFileContents] Loaded 1 files from cache: [1]: "F:/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/testref/entry-expasy.enzyme-1.1.1.54-content.txt".
biodb.DEBUG[2024-09-07 16:03:32.690][biodb$getFactory()$createEntryFromCo ...] Creating Expasy ENZYME database. entries from 1 content(s).
biodb.DEBUG[2024-09-07 16:03:32.692][biodb$getFactory()$createEntryFromCo ...] Parsing 1 Expasy ENZYME database. entries.
biodb.DEBUG[2024-09-07 16:03:32.693][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-07 16:03:32.694][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-07 16:03:32.696][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-07 16:03:32.703][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-07 16:03:32.704][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-07 16:03:32.705][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:32.706][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-07 16:03:32.708][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-07 16:03:32.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-07 16:03:32.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.714][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-09-07 16:03:32.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-09-07 16:03:32.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.719][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-07 16:03:32.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-07 16:03:32.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.724][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-09-07 16:03:32.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-09-07 16:03:32.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.729][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-09-07 16:03:32.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-09-07 16:03:32.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.734][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-09-07 16:03:32.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-09-07 16:03:32.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.739][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-07 16:03:32.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-07 16:03:32.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.744][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-09-07 16:03:32.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-09-07 16:03:32.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.753][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-07 16:03:32.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-07 16:03:32.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.758][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-07 16:03:32.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-07 16:03:32.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.763][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-07 16:03:32.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-07 16:03:32.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.768][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-07 16:03:32.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-07 16:03:32.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.773][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-07 16:03:32.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-07 16:03:32.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.778][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-07 16:03:32.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-07 16:03:32.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-07 16:03:32.783][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 1.1.1.54.
biodb.TRACE[2024-09-07 16:03:32.802][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-09-07 16:03:32.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-09-07 16:03:32.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.807][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-09-07 16:03:32.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-09-07 16:03:32.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.812][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-09-07 16:03:32.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-09-07 16:03:32.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.817][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-09-07 16:03:32.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-09-07 16:03:32.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.823][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-07 16:03:32.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-07 16:03:32.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.834][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-09-07 16:03:32.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-09-07 16:03:32.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.844][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-07 16:03:32.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-07 16:03:32.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.849][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-07 16:03:32.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-07 16:03:32.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.854][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-07 16:03:32.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-07 16:03:32.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.860][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-07 16:03:32.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-07 16:03:32.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.865][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-07 16:03:32.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-07 16:03:32.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.870][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-07 16:03:32.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-07 16:03:32.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.875][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-09-07 16:03:32.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-09-07 16:03:32.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.880][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-09-07 16:03:32.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-09-07 16:03:32.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.885][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-09-07 16:03:32.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-09-07 16:03:32.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.912][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-07 16:03:32.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-07 16:03:32.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.917][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-07 16:03:32.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-07 16:03:32.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.922][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-07 16:03:32.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-07 16:03:32.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.927][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-07 16:03:32.928][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-07 16:03:32.930][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.931][ef$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.932][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-07 16:03:32.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-07 16:03:32.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.947][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-07 16:03:32.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-07 16:03:32.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.952][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-07 16:03:32.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-07 16:03:32.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.957][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-07 16:03:32.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-07 16:03:32.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.962][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-07 16:03:32.963][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-07 16:03:32.964][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.965][ef$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.966][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-07 16:03:32.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-07 16:03:32.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.981][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-09-07 16:03:32.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-09-07 16:03:32.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.986][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-09-07 16:03:32.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-09-07 16:03:32.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.991][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-09-07 16:03:32.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-09-07 16:03:32.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:32.996][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-09-07 16:03:32.997][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-09-07 16:03:32.998][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:32.999][ef$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:33.000][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-09-07 16:03:33.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-09-07 16:03:33.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:33.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:33.015][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-07 16:03:33.016][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-07 16:03:33.017][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:33.019][ef$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:33.025][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-09-07 16:03:33.027][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-09-07 16:03:33.028][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:33.029][ef$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:33.035][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-07 16:03:33.037][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-07 16:03:33.038][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:33.039][ef$get] fields variable is a list.
biodb.INFO [2024-09-07 16:03:33.051][biodb::testThat]
biodb.INFO [2024-09-07 16:03:33.052][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-09-07 16:03:33.053][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-07 16:03:33.054][biodb::testThat]
biodb.DEBUG[2024-09-07 16:03:33.057][private$loadEntries] Creating entries from ids [2]: "1.1.1.1, 1.1.1.54".
biodb.DEBUG[2024-09-07 16:03:33.063][conn$getEntryContent] Get Expasy ENZYME database. entry content(s) for 2 id(s)...
biodb.TRACE[2024-09-07 16:03:33.083][cch$loadFileContent] Trying to load 2 files from cache: [2]: "1.1.1.1, 1.1.1.54".
biodb.INFO [2024-09-07 16:03:33.085][self$getFolderPath] Create cache folder "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280" for "expasy.enzyme-b59b84d962b6741050ba8f70ff4db280".
biodb.TRACE[2024-09-07 16:03:33.087][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2024-09-07 16:03:33.089][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-09-07 16:03:33.090][conn$getEntryContent] 0 Expasy ENZYME database. entry content(s) loaded from cache.
biodb.DEBUG[2024-09-07 16:03:33.092][conn$getEntryContent] 2 entry content(s) need to be fetched from Expasy ENZYME database. database "https://enzyme.expasy.org/".
biodb.DEBUG[2024-09-07 16:03:33.093][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-09-07 16:03:33.094][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-09-07 16:03:33.099][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-07 16:03:33.100][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-07 16:03:33.101][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-07 16:03:33.108][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-07 16:03:33.115][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-07 16:03:33.117][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:33.118][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-07 16:03:33.119][scheduler$sendRequest] Getting content of get URL request "https://enzyme.expasy.org/EC/1.1.1.1.txt".
biodb.DEBUG[2024-09-07 16:03:33.137][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-07 16:03:33.139][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-07 16:03:33.140][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/EC/1.1.1.1.txt".
biodb.TRACE[2024-09-07 16:03:33.805][doesRCurlRequestUrlExist] According to RCurl, URL https://enzyme.expasy.org/EC/1.1.1.1.txt does not exist.
biodb.TRACE[2024-09-07 16:03:33.807][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-09-07 16:03:33.808][getUrlRequestResult] URL "https://enzyme.expasy.org/EC/1.1.1.1.txt" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-09-07 16:03:33.809][getBaseUrlRequestResult] Using base::url() for sending request (https://enzyme.expasy.org/EC/1.1.1.1.txt).
biodb.DEBUG[2024-09-07 16:03:34.233][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-09-07 16:03:34.236][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a52675cfd2f0c2b41556caa64d9341e3.content"
biodb.TRACE[2024-09-07 16:03:34.250][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a52675cfd2f0c2b41556caa64d9341e3.request"
biodb.DEBUG[2024-09-07 16:03:34.254][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-07 16:03:34.255][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-07 16:03:34.256][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-07 16:03:34.263][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-07 16:03:34.265][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-07 16:03:34.266][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:34.267][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-07 16:03:34.285][scheduler$sendRequest] Getting content of get URL request "https://enzyme.expasy.org/EC/1.1.1.54.txt".
biodb.DEBUG[2024-09-07 16:03:34.299][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-07 16:03:34.300][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-07 16:03:34.319][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/EC/1.1.1.54.txt".
biodb.TRACE[2024-09-07 16:03:34.542][doesRCurlRequestUrlExist] According to RCurl, URL https://enzyme.expasy.org/EC/1.1.1.54.txt does not exist.
biodb.TRACE[2024-09-07 16:03:34.543][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-09-07 16:03:34.544][getUrlRequestResult] URL "https://enzyme.expasy.org/EC/1.1.1.54.txt" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-09-07 16:03:34.546][getBaseUrlRequestResult] Using base::url() for sending request (https://enzyme.expasy.org/EC/1.1.1.54.txt).
biodb.DEBUG[2024-09-07 16:03:34.962][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-09-07 16:03:34.965][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a9b93566a091cbe35a06e4b3871f95c9.content"
biodb.TRACE[2024-09-07 16:03:34.970][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a9b93566a091cbe35a06e4b3871f95c9.request"
biodb.TRACE[2024-09-07 16:03:34.974][private$doSaveContentToFile] Saving to cache [2]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/1.1.1.1.txt, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/1.1.1.54.txt"
biodb.DEBUG[2024-09-07 16:03:34.977][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-09-07 16:03:34.978][self$createEntryFromContent] Creating Expasy ENZYME database. entries from 2 content(s).
biodb.DEBUG[2024-09-07 16:03:34.980][self$createEntryFromContent] Parsing 2 Expasy ENZYME database. entries.
biodb.DEBUG[2024-09-07 16:03:34.982][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-07 16:03:34.983][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-07 16:03:34.984][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-07 16:03:34.991][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-07 16:03:34.992][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-07 16:03:34.993][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:34.994][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-07 16:03:34.997][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-07 16:03:34.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-07 16:03:35.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:35.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:35.002][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-09-07 16:03:35.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-09-07 16:03:35.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:35.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:35.008][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-07 16:03:35.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-07 16:03:35.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:35.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:35.013][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-09-07 16:03:35.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-09-07 16:03:35.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:35.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:35.018][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-07 16:03:35.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-07 16:03:35.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:35.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:35.023][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-07 16:03:35.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-07 16:03:35.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:35.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:35.028][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-07 16:03:35.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-07 16:03:35.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:35.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:35.033][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-07 16:03:35.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-07 16:03:35.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:35.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:35.038][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-07 16:03:35.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-07 16:03:35.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:35.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:35.043][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-09-07 16:03:35.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-09-07 16:03:35.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:35.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:35.048][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-09-07 16:03:35.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-09-07 16:03:35.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:35.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:35.053][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-07 16:03:35.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-07 16:03:35.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:35.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:35.057][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-09-07 16:03:35.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-09-07 16:03:35.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:35.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:35.062][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-07 16:03:35.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-07 16:03:35.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:35.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:35.067][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-07 16:03:35.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-07 16:03:35.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:35.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:35.072][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-07 16:03:35.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-07 16:03:35.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:35.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-07 16:03:35.078][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-07 16:03:35.079][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-07 16:03:35.080][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-07 16:03:35.092][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-07 16:03:35.093][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-07 16:03:35.094][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:35.096][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-07 16:03:35.098][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-07 16:03:35.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-07 16:03:35.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:35.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:35.103][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-09-07 16:03:35.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-09-07 16:03:35.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:35.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:35.109][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-07 16:03:35.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-07 16:03:35.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:35.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:35.114][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-09-07 16:03:35.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-09-07 16:03:35.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:35.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:35.119][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-09-07 16:03:35.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-09-07 16:03:35.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:35.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:35.124][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-09-07 16:03:35.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-09-07 16:03:35.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:35.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:35.129][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-07 16:03:35.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-07 16:03:35.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:35.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:35.134][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-09-07 16:03:35.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-09-07 16:03:35.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:35.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:35.139][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-07 16:03:35.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-07 16:03:35.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:35.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:35.144][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-07 16:03:35.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-07 16:03:35.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:35.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:35.149][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-07 16:03:35.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-07 16:03:35.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:35.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:35.154][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-07 16:03:35.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-07 16:03:35.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:35.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:35.159][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-07 16:03:35.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-07 16:03:35.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:35.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:35.164][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-07 16:03:35.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-07 16:03:35.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:35.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:35.169][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-07 16:03:35.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-07 16:03:35.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:35.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:35.174][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-07 16:03:35.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-07 16:03:35.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:35.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:35.178][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-07 16:03:35.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-07 16:03:35.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:35.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-07 16:03:35.183][self$createEntryFromContent] Accession numbers: 1.1.1.1, 1.1.1.54.
biodb.TRACE[2024-09-07 16:03:35.184][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-09-07 16:03:35.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-09-07 16:03:35.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:35.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:35.189][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-09-07 16:03:35.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-09-07 16:03:35.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:35.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:35.194][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-09-07 16:03:35.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-09-07 16:03:35.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:35.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:35.205][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-09-07 16:03:35.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-09-07 16:03:35.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:35.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:35.210][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-09-07 16:03:35.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-09-07 16:03:35.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:35.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:35.215][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-09-07 16:03:35.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-09-07 16:03:35.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:35.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-09-07 16:03:35.236][biodb::testThat]
biodb.INFO [2024-09-07 16:03:35.237][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-09-07 16:03:35.238][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-07 16:03:35.239][biodb::testThat]
biodb.TRACE[2024-09-07 16:03:35.243][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-07 16:03:35.244][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-07 16:03:35.245][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:35.246][ef$get] fields variable is a list.
biodb.DEBUG[2024-09-07 16:03:35.248][function(conn, opt)] Testing searchForEntries() with entry "1.1.1.1" and field "name".
biodb.TRACE[2024-09-07 16:03:35.277][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-07 16:03:35.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-07 16:03:35.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:35.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:35.283][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-07 16:03:35.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-07 16:03:35.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:35.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:35.288][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-07 16:03:35.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-07 16:03:35.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:35.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-07 16:03:35.295][function(conn, opt)] With value "alcohol dehydrogenase".
biodb.DEBUG[2024-09-07 16:03:35.298][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://enzyme.expasy.org/enzyme-byname.html?alcohol dehydrogenase".
biodb.DEBUG[2024-09-07 16:03:35.301][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-09-07 16:03:35.302][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-09-07 16:03:35.303][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase".
biodb.TRACE[2024-09-07 16:03:35.526][doesRCurlRequestUrlExist] According to RCurl, URL https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase does not exist.
biodb.TRACE[2024-09-07 16:03:35.528][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-09-07 16:03:35.530][getUrlRequestResult] URL "https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-09-07 16:03:35.531][getBaseUrlRequestResult] Using base::url() for sending request (https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase).
biodb.DEBUG[2024-09-07 16:03:35.973][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-09-07 16:03:35.976][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.content"
biodb.TRACE[2024-09-07 16:03:35.981][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.request"
biodb.DEBUG[2024-09-07 16:03:35.988][function(conn, opt)] With found IDs [1]: "1.1.1.1".
biodb.INFO [2024-09-07 16:03:36.012][biodb::testThat]
biodb.INFO [2024-09-07 16:03:36.013][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-09-07 16:03:36.014][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-07 16:03:36.015][biodb::testThat]
biodb.TRACE[2024-09-07 16:03:36.048][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-07 16:03:36.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-07 16:03:36.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:36.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:36.053][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-07 16:03:36.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-07 16:03:36.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:36.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:36.058][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-07 16:03:36.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-07 16:03:36.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:36.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-07 16:03:36.089][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://enzyme.expasy.org/enzyme-byname.html?alcohol dehydrogenase".
biodb.DEBUG[2024-09-07 16:03:36.093][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-09-07 16:03:36.107][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f603fa2a57aec59588edc37541c6f6d5".
biodb.TRACE[2024-09-07 16:03:36.109][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-07 16:03:36.114][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.content".
biodb.INFO [2024-09-07 16:03:36.139][biodb::testThat]
biodb.INFO [2024-09-07 16:03:36.141][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-09-07 16:03:36.142][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-07 16:03:36.143][biodb::testThat]
biodb.TRACE[2024-09-07 16:03:36.162][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-09-07 16:03:36.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-09-07 16:03:36.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:36.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:36.168][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-09-07 16:03:36.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-09-07 16:03:36.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:36.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:36.173][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-09-07 16:03:36.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-09-07 16:03:36.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:36.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:36.178][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-09-07 16:03:36.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-09-07 16:03:36.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:36.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:36.211][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-09-07 16:03:36.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-09-07 16:03:36.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:36.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:36.217][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-09-07 16:03:36.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-09-07 16:03:36.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:36.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:36.222][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-09-07 16:03:36.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-09-07 16:03:36.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:36.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:36.227][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-09-07 16:03:36.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-09-07 16:03:36.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:36.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-09-07 16:03:36.240][biodb::testThat]
biodb.INFO [2024-09-07 16:03:36.241][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-09-07 16:03:36.242][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-07 16:03:36.243][biodb::testThat]
biodb.INFO [2024-09-07 16:03:36.256][biodb::testThat]
biodb.INFO [2024-09-07 16:03:36.257][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-09-07 16:03:36.258][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-07 16:03:36.260][biodb::testThat]
biodb.INFO [2024-09-07 16:03:36.278][biodb::testThat]
biodb.INFO [2024-09-07 16:03:36.279][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-09-07 16:03:36.281][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-07 16:03:36.282][biodb::testThat]
biodb.DEBUG[2024-09-07 16:03:36.295][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[2024-09-07 16:03:36.521][getUrlContent] Use base::url() for downloading content of URL https://enzyme.expasy.org/cgi-bin/enzyme/enzyme-search-ec?field1=1&field2=1&field3=1&field4=1.
biodb.INFO [2024-09-07 16:03:36.971][biodb::testThat]
biodb.INFO [2024-09-07 16:03:36.973][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-09-07 16:03:36.974][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-07 16:03:36.975][biodb::testThat]
biodb.DEBUG[2024-09-07 16:03:37.200][getUrlContent] Use base::url() for downloading content of URL https://enzyme.expasy.org/images/1.1.1.1/image.png.
biodb.TRACE[2024-09-07 16:03:37.653][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-07 16:03:37.655][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-07 16:03:37.656][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:37.658][ef$get] fields variable is a list.
biodb.TRACE[2024-09-07 16:03:37.659][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-07 16:03:37.660][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-07 16:03:37.661][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-07 16:03:37.663][ef$get] fields variable is a list.
biodb.INFO [2024-09-07 16:03:37.664][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-09-07 16:03:37.666][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector expasy.enzyme from the request scheduler
biodb.INFO [2024-09-07 16:03:37.668][self$deleteConn] Connector "expasy.enzyme" deleted.
biodb.DEBUG[2024-09-07 16:03:37.669][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-09-07 16:03:37.670][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-07 16:03:37.671][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-07 16:03:37.672][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-07 16:03:37.673][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-07 16:03:37.674][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:37.675][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-09-07 16:03:37.686][biodb::testContext]
biodb.INFO [2024-09-07 16:03:37.687][biodb::testContext] ********************************************************************************
biodb.INFO [2024-09-07 16:03:37.688][biodb::testContext] Test context - Example long tests
biodb.INFO [2024-09-07 16:03:37.689][biodb::testContext] ********************************************************************************
biodb.INFO [2024-09-07 16:03:37.690][biodb::testContext]
biodb.INFO [2024-09-07 16:03:37.693][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.13.0.
biodb.DEBUG[2024-09-07 16:03:37.696][self$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.20-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2024-09-07 16:03:37.702][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-09-07 16:03:37.703][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-09-07 16:03:37.704][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-09-07 16:03:37.705][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:37.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:37.707][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-07 16:03:37.714][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-09-07 16:03:37.716][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-09-07 16:03:37.717][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:37.718][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:37.720][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-07 16:03:37.721][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-09-07 16:03:37.722][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-09-07 16:03:37.723][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:37.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:37.725][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-07 16:03:37.727][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-09-07 16:03:37.728][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-09-07 16:03:37.729][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-09-07 16:03:37.730][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:37.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:37.732][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-07 16:03:37.734][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-09-07 16:03:37.735][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-09-07 16:03:37.736][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-09-07 16:03:37.737][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:37.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:37.739][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-07 16:03:37.741][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-09-07 16:03:37.742][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-09-07 16:03:37.743][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:37.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:37.745][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-07 16:03:37.746][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-09-07 16:03:37.748][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-09-07 16:03:37.749][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-09-07 16:03:37.750][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:37.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:37.752][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-07 16:03:37.754][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-09-07 16:03:37.755][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-09-07 16:03:37.756][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:37.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:37.758][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-07 16:03:37.759][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-09-07 16:03:37.761][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-09-07 16:03:37.762][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-09-07 16:03:37.763][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:37.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:37.765][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-07 16:03:37.766][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-09-07 16:03:37.768][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-09-07 16:03:37.769][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-09-07 16:03:37.770][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-09-07 16:03:37.771][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-09-07 16:03:37.773][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-09-07 16:03:37.774][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:37.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:37.776][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-07 16:03:37.777][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-09-07 16:03:37.778][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-09-07 16:03:37.779][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:37.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:37.782][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[2024-09-07 16:03:37.783][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-09-07 16:03:37.784][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-09-07 16:03:37.785][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:37.786][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:37.787][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-07 16:03:37.789][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-09-07 16:03:37.790][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-09-07 16:03:37.791][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:37.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:37.793][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[2024-09-07 16:03:37.794][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-09-07 16:03:37.796][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-09-07 16:03:37.797][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:37.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:37.799][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-07 16:03:37.800][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-09-07 16:03:37.801][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-09-07 16:03:37.803][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:37.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:37.805][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[2024-09-07 16:03:37.806][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-09-07 16:03:37.807][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-09-07 16:03:37.811][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-09-07 16:03:37.812][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:37.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:37.814][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-07 16:03:37.815][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-09-07 16:03:37.816][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-09-07 16:03:37.818][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-09-07 16:03:37.819][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:37.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:37.821][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[2024-09-07 16:03:37.822][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-09-07 16:03:37.824][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-09-07 16:03:37.826][self$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[2024-09-07 16:03:37.827][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-09-07 16:03:37.828][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-09-07 16:03:37.829][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-09-07 16:03:37.831][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-09-07 16:03:37.832][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-09-07 16:03:37.833][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-09-07 16:03:37.834][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-09-07 16:03:37.835][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-09-07 16:03:37.842][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-09-07 16:03:37.843][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-09-07 16:03:37.844][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-09-07 16:03:37.845][self$setPropertyValue]
biodb.DEBUG[2024-09-07 16:03:37.847][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-09-07 16:03:37.848][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-09-07 16:03:37.848][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-09-07 16:03:37.848][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-09-07 16:03:37.848][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-09-07 16:03:37.848][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-09-07 16:03:37.849][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-09-07 16:03:37.850][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-07 16:03:37.851][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-07 16:03:37.853][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-09-07 16:03:37.854][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-07 16:03:37.855][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-07 16:03:37.856][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-09-07 16:03:37.857][self$setPropertyValue]
biodb.DEBUG[2024-09-07 16:03:37.858][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-09-07 16:03:37.860][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-09-07 16:03:37.861][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-09-07 16:03:37.862][self$setPropertyValue]
biodb.DEBUG[2024-09-07 16:03:37.863][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-09-07 16:03:37.865][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-09-07 16:03:37.867][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-09-07 16:03:37.868][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-09-07 16:03:37.869][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-09-07 16:03:37.870][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-09-07 16:03:37.871][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-09-07 16:03:37.873][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-09-07 16:03:37.874][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-09-07 16:03:37.875][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-09-07 16:03:37.876][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-09-07 16:03:37.878][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-09-07 16:03:37.879][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-09-07 16:03:37.880][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-09-07 16:03:37.881][self$setPropertyValue]
biodb.DEBUG[2024-09-07 16:03:37.883][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-09-07 16:03:37.884][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-09-07 16:03:37.884][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-09-07 16:03:37.884][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-09-07 16:03:37.884][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-09-07 16:03:37.884][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-09-07 16:03:37.885][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-09-07 16:03:37.886][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-07 16:03:37.887][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-07 16:03:37.889][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-09-07 16:03:37.890][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-07 16:03:37.891][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-07 16:03:37.892][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-09-07 16:03:37.893][self$setPropertyValue]
biodb.DEBUG[2024-09-07 16:03:37.894][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-09-07 16:03:37.895][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-09-07 16:03:37.897][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-09-07 16:03:37.898][self$setPropertyValue]
biodb.DEBUG[2024-09-07 16:03:37.899][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-09-07 16:03:37.901][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-09-07 16:03:37.902][self$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[2024-09-07 16:03:37.904][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-09-07 16:03:37.905][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-09-07 16:03:37.906][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-09-07 16:03:37.907][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-09-07 16:03:37.908][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-09-07 16:03:37.910][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-09-07 16:03:37.911][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-09-07 16:03:37.912][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-09-07 16:03:37.913][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-09-07 16:03:37.915][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-09-07 16:03:37.916][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-09-07 16:03:37.917][self$setPropertyValue]
biodb.DEBUG[2024-09-07 16:03:37.918][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-09-07 16:03:37.919][self$setPropertyValue]
biodb.DEBUG[2024-09-07 16:03:37.921][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-09-07 16:03:37.922][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-07 16:03:37.923][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-07 16:03:37.924][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-09-07 16:03:37.925][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-07 16:03:37.926][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-07 16:03:37.927][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-09-07 16:03:37.929][self$setPropertyValue]
biodb.DEBUG[2024-09-07 16:03:37.930][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-09-07 16:03:37.931][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-09-07 16:03:37.932][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-09-07 16:03:37.933][self$setPropertyValue]
biodb.DEBUG[2024-09-07 16:03:37.935][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-09-07 16:03:37.937][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-09-07 16:03:37.938][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-09-07 16:03:37.939][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-09-07 16:03:37.940][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-09-07 16:03:37.941][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-09-07 16:03:37.943][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-09-07 16:03:37.944][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-09-07 16:03:37.945][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-09-07 16:03:37.946][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-09-07 16:03:37.947][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-09-07 16:03:37.949][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-09-07 16:03:37.950][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-09-07 16:03:37.951][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-09-07 16:03:37.952][self$setPropertyValue]
biodb.DEBUG[2024-09-07 16:03:37.953][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-09-07 16:03:37.955][self$setPropertyValue]
biodb.DEBUG[2024-09-07 16:03:37.956][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-09-07 16:03:37.957][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-07 16:03:37.958][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-07 16:03:37.964][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-09-07 16:03:37.966][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-07 16:03:37.967][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-07 16:03:37.968][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-09-07 16:03:37.969][self$setPropertyValue]
biodb.DEBUG[2024-09-07 16:03:37.970][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-09-07 16:03:37.971][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-09-07 16:03:37.973][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-09-07 16:03:37.974][self$setPropertyValue]
biodb.DEBUG[2024-09-07 16:03:37.975][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-09-07 16:03:37.976][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:37.977][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-07 16:03:37.979][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:37.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-07 16:03:37.981][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-07 16:03:37.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:37.983][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-07 16:03:37.984][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:37.985][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-07 16:03:37.986][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-07 16:03:37.987][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:37.988][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-07 16:03:37.990][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:37.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-07 16:03:37.992][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-07 16:03:37.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:37.994][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-07 16:03:37.995][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:37.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-07 16:03:37.997][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-07 16:03:37.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:38.000][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-07 16:03:38.001][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:38.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-07 16:03:38.003][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-07 16:03:38.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:38.005][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-07 16:03:38.006][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:38.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-07 16:03:38.008][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-07 16:03:38.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:38.011][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-07 16:03:38.012][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:38.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-07 16:03:38.014][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-07 16:03:38.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:38.016][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-07 16:03:38.017][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:38.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-07 16:03:38.020][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-07 16:03:38.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:38.022][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-07 16:03:38.023][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:38.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-07 16:03:38.025][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-07 16:03:38.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:38.027][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-07 16:03:38.028][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:38.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-07 16:03:38.031][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-07 16:03:38.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:38.033][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-07 16:03:38.034][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:38.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-07 16:03:38.036][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-07 16:03:38.037][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:38.038][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-07 16:03:38.039][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:38.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-07 16:03:38.041][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-07 16:03:38.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:38.044][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-07 16:03:38.045][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:38.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-07 16:03:38.047][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-07 16:03:38.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:38.049][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-07 16:03:38.050][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:38.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-07 16:03:38.052][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-07 16:03:38.053][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:38.055][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-07 16:03:38.056][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:38.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-07 16:03:38.058][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-07 16:03:38.059][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:38.060][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-07 16:03:38.061][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:38.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-07 16:03:38.063][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-07 16:03:38.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:38.066][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-07 16:03:38.067][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:38.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-07 16:03:38.069][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-07 16:03:38.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:38.071][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[2024-09-07 16:03:38.072][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-09-07 16:03:38.074][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-09-07 16:03:38.076][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-09-07 16:03:38.077][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-09-07 16:03:38.079][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-09-07 16:03:38.080][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-09-07 16:03:38.087][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-09-07 16:03:38.089][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-09-07 16:03:38.090][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-09-07 16:03:38.092][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-09-07 16:03:38.093][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-09-07 16:03:38.095][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-09-07 16:03:38.096][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-09-07 16:03:38.098][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-09-07 16:03:38.100][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-09-07 16:03:38.101][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-09-07 16:03:38.103][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-09-07 16:03:38.104][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-09-07 16:03:38.106][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-09-07 16:03:38.108][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-09-07 16:03:38.109][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-09-07 16:03:38.111][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-09-07 16:03:38.112][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-09-07 16:03:38.114][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-09-07 16:03:38.115][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-09-07 16:03:38.117][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-09-07 16:03:38.119][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-09-07 16:03:38.120][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-09-07 16:03:38.122][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-09-07 16:03:38.124][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-09-07 16:03:38.125][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-09-07 16:03:38.127][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-09-07 16:03:38.128][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-09-07 16:03:38.130][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-09-07 16:03:38.131][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-09-07 16:03:38.133][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-09-07 16:03:38.135][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-09-07 16:03:38.136][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-09-07 16:03:38.138][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-09-07 16:03:38.139][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-09-07 16:03:38.141][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-09-07 16:03:38.143][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-09-07 16:03:38.144][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-09-07 16:03:38.146][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-09-07 16:03:38.147][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-09-07 16:03:38.149][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-09-07 16:03:38.150][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-09-07 16:03:38.152][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-09-07 16:03:38.154][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-09-07 16:03:38.155][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-09-07 16:03:38.157][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-09-07 16:03:38.158][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-09-07 16:03:38.160][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-09-07 16:03:38.161][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-09-07 16:03:38.163][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-09-07 16:03:38.165][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-09-07 16:03:38.166][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-09-07 16:03:38.168][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-09-07 16:03:38.169][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-09-07 16:03:38.171][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-09-07 16:03:38.172][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-09-07 16:03:38.174][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-09-07 16:03:38.176][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-09-07 16:03:38.177][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-09-07 16:03:38.179][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-09-07 16:03:38.180][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-09-07 16:03:38.182][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-09-07 16:03:38.183][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-09-07 16:03:38.185][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-09-07 16:03:38.187][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-09-07 16:03:38.188][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-09-07 16:03:38.190][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-09-07 16:03:38.191][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-09-07 16:03:38.198][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-09-07 16:03:38.200][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-09-07 16:03:38.201][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-09-07 16:03:38.203][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-09-07 16:03:38.205][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-09-07 16:03:38.206][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-09-07 16:03:38.208][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-09-07 16:03:38.209][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-09-07 16:03:38.211][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-09-07 16:03:38.212][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-09-07 16:03:38.214][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-09-07 16:03:38.217][initialize] This is biodb version 1.13.0.
biodb.DEBUG[2024-09-07 16:03:38.218][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-09-07 16:03:38.219][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-09-07 16:03:38.220][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-07 16:03:38.221][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:38.222][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-07 16:03:38.224][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:38.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-07 16:03:38.226][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-07 16:03:38.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-07 16:03:38.228][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-07 16:03:38.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:38.230][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-07 16:03:38.231][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:38.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-07 16:03:38.234][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-07 16:03:38.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-07 16:03:38.236][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-07 16:03:38.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:38.238][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-07 16:03:38.239][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:38.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-07 16:03:38.241][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-07 16:03:38.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-07 16:03:38.244][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-07 16:03:38.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:38.246][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-07 16:03:38.247][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:38.248][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-07 16:03:38.249][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-07 16:03:38.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-07 16:03:38.251][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-07 16:03:38.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:38.254][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-07 16:03:38.255][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:38.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-07 16:03:38.257][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-07 16:03:38.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-07 16:03:38.259][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-07 16:03:38.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:38.261][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-07 16:03:38.263][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:38.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-07 16:03:38.265][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-07 16:03:38.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-07 16:03:38.267][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-07 16:03:38.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:38.269][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-07 16:03:38.270][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:38.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-07 16:03:38.272][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-07 16:03:38.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-07 16:03:38.275][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-07 16:03:38.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:38.277][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-07 16:03:38.278][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:38.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-07 16:03:38.280][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-07 16:03:38.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-07 16:03:38.282][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-07 16:03:38.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:38.285][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-07 16:03:38.286][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:38.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-07 16:03:38.288][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-07 16:03:38.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-07 16:03:38.290][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-07 16:03:38.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:38.292][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-07 16:03:38.294][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:38.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-07 16:03:38.296][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-07 16:03:38.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-07 16:03:38.298][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-07 16:03:38.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:38.300][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-07 16:03:38.302][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:38.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-07 16:03:38.304][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-07 16:03:38.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-07 16:03:38.306][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-07 16:03:38.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:38.308][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-07 16:03:38.309][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:38.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-07 16:03:38.312][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-07 16:03:38.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-07 16:03:38.314][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-07 16:03:38.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:38.321][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-07 16:03:38.323][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:38.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-07 16:03:38.325][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-07 16:03:38.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-07 16:03:38.327][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-07 16:03:38.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:38.329][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-07 16:03:38.330][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:38.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-07 16:03:38.332][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-07 16:03:38.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-07 16:03:38.335][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-07 16:03:38.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:38.337][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-07 16:03:38.338][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:38.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-07 16:03:38.340][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-07 16:03:38.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-07 16:03:38.342][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-07 16:03:38.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:38.345][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-07 16:03:38.346][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:38.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-07 16:03:38.348][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-07 16:03:38.349][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-07 16:03:38.350][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-07 16:03:38.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:38.352][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-07 16:03:38.354][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-07 16:03:38.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-07 16:03:38.356][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-07 16:03:38.357][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-07 16:03:38.358][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-07 16:03:38.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:38.360][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-07 16:03:38.364][biodb$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/definitions.yml".
biodb.DEBUG[2024-09-07 16:03:38.366][self$getDbsInfo()$define] Define connector expasy.enzyme.
biodb.DEBUG[2024-09-07 16:03:38.368][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-09-07 16:03:38.369][self$setPropertyValue] Setting property "description" to "Write here the description of this database.".
biodb.DEBUG[2024-09-07 16:03:38.371][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-09-07 16:03:38.372][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-09-07 16:03:38.373][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-09-07 16:03:38.374][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-09-07 16:03:38.376][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-09-07 16:03:38.377][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-09-07 16:03:38.378][self$setPropertyValue] Setting property "entry.content.type" to "txt".
biodb.DEBUG[2024-09-07 16:03:38.379][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-09-07 16:03:38.381][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-09-07 16:03:38.382][self$setPropertyValue] Setting property "name" to "Expasy ENZYME database.".
biodb.DEBUG[2024-09-07 16:03:38.383][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-09-07 16:03:38.384][self$setPropertyValue] Setting property "parsing.expr" to "^ID\s+([0-9.]+)$".
biodb.DEBUG[2024-09-07 16:03:38.384][self$setPropertyValue] Setting property "parsing.expr" to "^CA\s+(.+?)\.?$".
biodb.DEBUG[2024-09-07 16:03:38.384][self$setPropertyValue] Setting property "parsing.expr" to "^CF\s+(.+?)\.?$".
biodb.DEBUG[2024-09-07 16:03:38.384][self$setPropertyValue] Setting property "parsing.expr" to "^DE\s+(.+?)\.?$".
biodb.DEBUG[2024-09-07 16:03:38.385][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-09-07 16:03:38.387][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-09-07 16:03:38.388][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-09-07 16:03:38.389][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-07 16:03:38.390][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-07 16:03:38.391][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-09-07 16:03:38.392][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-07 16:03:38.394][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-07 16:03:38.395][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-09-07 16:03:38.396][self$setPropertyValue] Setting property "urls" to "https://enzyme.expasy.org/".
biodb.DEBUG[2024-09-07 16:03:38.397][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-09-07 16:03:38.398][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-09-07 16:03:38.399][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-09-07 16:03:38.401][self$setPropertyValue]
biodb.DEBUG[2024-09-07 16:03:38.402][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-09-07 16:03:38.406][super$initialize] Initialize connector expasy.enzyme.
biodb.DEBUG[2024-09-07 16:03:38.407][super$initialize] Register connector expasy.enzyme with the request scheduler
biodb.DEBUG[2024-09-07 16:03:38.408][private$bdb$getRequestScheduler()$re ...] Register connector expasy.enzyme.
biodb.DEBUG[2024-09-07 16:03:38.410][private$addConnectorRules] Create new rule for URL "enzyme.expasy.org" of connector "expasy.enzyme".
biodb.DEBUG[2024-09-07 16:03:38.412][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-09-07 16:03:38.413][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-09-07 16:03:38.414][biodb$getFactory()$createConn] Creating new connector expasy.enzyme for database class expasy.enzyme .
biodb.INFO [2024-09-07 16:03:38.415][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-09-07 16:03:38.417][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector expasy.enzyme from the request scheduler
biodb.INFO [2024-09-07 16:03:38.418][self$deleteConn] Connector "expasy.enzyme" deleted.
biodb.DEBUG[2024-09-07 16:03:38.419][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-09-07 16:03:38.420][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-07 16:03:38.421][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-07 16:03:38.422][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-07 16:03:38.424][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-07 16:03:38.425][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-09-07 16:03:38.426][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 85 ]

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

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

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbExpasy_1.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck'
* using R version 4.4.1 (2024-06-14 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using options '--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error'
* checking for file 'biodbExpasy/DESCRIPTION' ... OK
* this is package 'biodbExpasy' version '1.9.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'biodbExpasy' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... SKIPPED
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in 'vignettes' ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in 'longtests' ... OK
* checking tests in 'longtests' ...
  Running 'testthat.R'
 ERROR
Running the tests in 'longtests/testthat.R' failed.
Last 13 lines of output:
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_long_100_generic.R:37:1'): The entry image URL can be downloaded. ──
  Error in `charToRaw(content)`: argument must be a character vector of length 1
  Backtrace:
      ▆
   1. ├─base::do.call(fct, params)
   2. └─biodb (local) `<fn>`(conn = `<ExpsyEnC>`, opt = `<named list>`)
   3.   └─biodb:::getUrlContent(url, binary = TRUE)
   4.     └─biodb:::getBaseUrlContent(u, binary = binary)
   5.       └─base::charToRaw(content)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 85 ]
  Error: Test failures
  Execution halted
* DONE

Status: 1 ERROR, 1 NOTE
See
  'F:/biocbuild/bbs-3.20-bioc-longtests/meat/biodbExpasy.Rcheck/00check.log'
for details.

Installation output

biodbExpasy.Rcheck/00install.out

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