Back to Long Tests report for BioC 3.19

This page was generated on 2024-06-08 23:55 -0400 (Sat, 08 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4755
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4489
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4520
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 7/33HostnameOS / ArchCHECK
biodbExpasy 1.8.0  (landing page)
Pierrick Roger
Snapshot Date: 2024-06-08 09:55 -0400 (Sat, 08 Jun 2024)
git_url: https://git.bioconductor.org/packages/biodbExpasy
git_branch: RELEASE_3_19
git_last_commit: de004e8
git_last_commit_date: 2024-04-30 11:41:12 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  ERROR  
palomino3Windows Server 2022 Datacenter / x64  ERROR  
lconwaymacOS 12.7.1 Monterey / x86_64  ERROR  

CHECK results for biodbExpasy on lconway

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

raw results


Summary

Package: biodbExpasy
Version: 1.8.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbExpasy_1.8.0.tar.gz
StartedAt: 2024-06-08 16:01:11 -0400 (Sat, 08 Jun 2024)
EndedAt: 2024-06-08 16:05:54 -0400 (Sat, 08 Jun 2024)
EllapsedTime: 283.7 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbExpasy.Rcheck
Warnings: NA

Tests output

biodbExpasy.Rcheck/tests/testthat.Rout.fail


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

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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbExpasy)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbExpasy")
biodb.INFO [2024-06-08 16:01:43.943][biodb::testContext]
biodb.INFO [2024-06-08 16:01:43.946][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-08 16:01:43.947][biodb::testContext] Test context - Generic long tests
biodb.INFO [2024-06-08 16:01:43.948][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-08 16:01:43.949][biodb::testContext]
biodb.INFO [2024-06-08 16:01:43.954][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-06-08 16:01:43.955][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-06-08 16:01:43.961][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-08 16:01:43.962][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-06-08 16:01:43.963][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-06-08 16:01:43.964][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:01:43.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:01:43.965][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:01:43.966][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-06-08 16:01:43.991][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-06-08 16:01:43.992][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:01:43.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:01:43.993][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:01:43.994][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-06-08 16:01:43.995][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-06-08 16:01:43.995][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:01:43.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:01:43.997][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:01:43.997][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-06-08 16:01:43.998][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-06-08 16:01:43.999][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-06-08 16:01:43.999][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:01:44.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:01:44.001][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:01:44.001][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-06-08 16:01:44.002][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-06-08 16:01:44.003][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-06-08 16:01:44.003][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:01:44.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:01:44.004][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:01:44.005][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-06-08 16:01:44.006][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-06-08 16:01:44.006][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:01:44.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:01:44.008][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:01:44.008][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-06-08 16:01:44.009][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-06-08 16:01:44.010][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-06-08 16:01:44.010][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:01:44.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:01:44.012][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:01:44.012][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-06-08 16:01:44.013][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-06-08 16:01:44.014][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:01:44.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:01:44.015][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:01:44.015][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-06-08 16:01:44.016][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-06-08 16:01:44.017][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-06-08 16:01:44.018][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:01:44.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:01:44.019][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:01:44.019][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-06-08 16:01:44.020][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-06-08 16:01:44.021][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-06-08 16:01:44.022][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-06-08 16:01:44.022][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-06-08 16:01:44.023][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-06-08 16:01:44.024][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:01:44.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:01:44.025][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:01:44.026][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-06-08 16:01:44.026][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-06-08 16:01:44.027][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:01:44.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:01:44.028][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:01:44.029][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-06-08 16:01:44.030][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-06-08 16:01:44.030][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:01:44.031][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:01:44.031][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:01:44.032][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-06-08 16:01:44.033][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-06-08 16:01:44.034][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:01:44.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:01:44.035][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:01:44.035][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-06-08 16:01:44.036][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-06-08 16:01:44.037][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:01:44.037][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:01:44.038][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[2024-06-08 16:01:44.039][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-06-08 16:01:44.039][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-06-08 16:01:44.040][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:01:44.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:01:44.041][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:01:44.042][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-06-08 16:01:44.043][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-06-08 16:01:44.059][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-06-08 16:01:44.059][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:01:44.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:01:44.061][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:01:44.061][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-06-08 16:01:44.062][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-06-08 16:01:44.063][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-06-08 16:01:44.063][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:01:44.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:01:44.065][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:01:44.067][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-06-08 16:01:44.090][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-08 16:01:44.101][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-06-08 16:01:44.101][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-08 16:01:44.102][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-08 16:01:44.103][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-08 16:01:44.104][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-08 16:01:44.104][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-08 16:01:44.105][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-08 16:01:44.106][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-08 16:01:44.106][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-08 16:01:44.107][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-08 16:01:44.108][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-06-08 16:01:44.109][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-08 16:01:44.109][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:01:44.110][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-08 16:01:44.111][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-08 16:01:44.111][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-08 16:01:44.111][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-08 16:01:44.111][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-08 16:01:44.111][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-08 16:01:44.112][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-08 16:01:44.112][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-08 16:01:44.113][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-08 16:01:44.114][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-08 16:01:44.114][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-08 16:01:44.115][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-08 16:01:44.116][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-08 16:01:44.116][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:01:44.117][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-08 16:01:44.118][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-08 16:01:44.118][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-08 16:01:44.119][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:01:44.120][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-06-08 16:01:44.121][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-08 16:01:44.122][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-06-08 16:01:44.123][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-08 16:01:44.123][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-08 16:01:44.124][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-08 16:01:44.125][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-08 16:01:44.125][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-08 16:01:44.126][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-08 16:01:44.127][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-08 16:01:44.127][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-08 16:01:44.128][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-08 16:01:44.129][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-06-08 16:01:44.130][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-08 16:01:44.130][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:01:44.131][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-08 16:01:44.132][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-08 16:01:44.132][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-08 16:01:44.132][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-08 16:01:44.132][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-08 16:01:44.132][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-08 16:01:44.137][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-08 16:01:44.137][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-08 16:01:44.138][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-08 16:01:44.139][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-08 16:01:44.139][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-08 16:01:44.140][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-08 16:01:44.141][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-08 16:01:44.141][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:01:44.142][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-08 16:01:44.143][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-08 16:01:44.143][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-08 16:01:44.144][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:01:44.145][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-06-08 16:01:44.146][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-08 16:01:44.147][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-06-08 16:01:44.148][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-08 16:01:44.148][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-08 16:01:44.149][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-08 16:01:44.150][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-08 16:01:44.150][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-08 16:01:44.151][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-08 16:01:44.152][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-08 16:01:44.152][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-08 16:01:44.153][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-08 16:01:44.154][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-06-08 16:01:44.154][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-08 16:01:44.155][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:01:44.156][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-08 16:01:44.157][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:01:44.157][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-08 16:01:44.158][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-08 16:01:44.159][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-08 16:01:44.159][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-08 16:01:44.160][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-08 16:01:44.161][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-08 16:01:44.161][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-08 16:01:44.162][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:01:44.163][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-08 16:01:44.163][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-08 16:01:44.164][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-08 16:01:44.165][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:01:44.165][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-06-08 16:01:44.167][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-08 16:01:44.167][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-06-08 16:01:44.168][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-08 16:01:44.169][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-08 16:01:44.170][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-08 16:01:44.170][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-08 16:01:44.171][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-08 16:01:44.172][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-08 16:01:44.172][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-08 16:01:44.173][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-08 16:01:44.174][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-08 16:01:44.175][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-06-08 16:01:44.175][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-08 16:01:44.176][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:01:44.177][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-08 16:01:44.177][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:01:44.178][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-08 16:01:44.179][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-08 16:01:44.179][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-08 16:01:44.180][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-08 16:01:44.181][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-08 16:01:44.181][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-08 16:01:44.182][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-08 16:01:44.183][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:01:44.183][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-08 16:01:44.184][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-08 16:01:44.185][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-08 16:01:44.185][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:01:44.188][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-08 16:01:44.189][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:01:44.189][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[2024-06-08 16:01:44.190][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:01:44.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:01:44.191][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:01:44.192][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:01:44.192][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:01:44.193][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:01:44.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:01:44.194][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:01:44.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:01:44.196][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:01:44.196][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:01:44.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:01:44.197][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:01:44.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:01:44.199][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:01:44.199][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:01:44.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:01:44.201][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:01:44.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:01:44.202][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:01:44.202][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:01:44.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:01:44.204][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:01:44.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:01:44.205][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:01:44.206][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:01:44.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:01:44.207][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:01:44.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:01:44.208][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:01:44.209][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:01:44.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:01:44.210][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:01:44.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:01:44.211][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:01:44.212][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:01:44.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:01:44.213][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:01:44.214][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:01:44.214][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:01:44.215][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:01:44.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:01:44.216][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:01:44.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:01:44.217][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:01:44.218][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:01:44.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:01:44.219][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:01:44.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:01:44.221][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:01:44.221][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:01:44.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:01:44.223][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:01:44.223][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:01:44.224][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:01:44.224][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:01:44.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:01:44.226][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:01:44.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:01:44.227][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:01:44.228][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:01:44.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:01:44.229][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:01:44.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:01:44.230][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[2024-06-08 16:01:44.231][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:01:44.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:01:44.232][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:01:44.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:01:44.233][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:01:44.234][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:01:44.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:01:44.235][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:01:44.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:01:44.236][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:01:44.237][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:01:44.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:01:44.238][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:01:44.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:01:44.240][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:01:44.240][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:01:44.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:01:44.241][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:01:44.242][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:01:44.243][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:01:44.243][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-06-08 16:01:44.247][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-06-08 16:01:44.248][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-06-08 16:01:44.249][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-06-08 16:01:44.250][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-08 16:01:44.251][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-08 16:01:44.252][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-06-08 16:01:44.253][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-06-08 16:01:44.254][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-08 16:01:44.255][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-08 16:01:44.256][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-08 16:01:44.257][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-06-08 16:01:44.258][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-06-08 16:01:44.259][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-06-08 16:01:44.260][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-06-08 16:01:44.261][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-08 16:01:44.262][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-06-08 16:01:44.263][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-06-08 16:01:44.264][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-08 16:01:44.265][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-06-08 16:01:44.266][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-06-08 16:01:44.267][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-06-08 16:01:44.272][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-06-08 16:01:44.273][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-06-08 16:01:44.274][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-06-08 16:01:44.275][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-06-08 16:01:44.276][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-06-08 16:01:44.277][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-06-08 16:01:44.278][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-06-08 16:01:44.279][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-06-08 16:01:44.280][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-06-08 16:01:44.281][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-06-08 16:01:44.281][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-06-08 16:01:44.282][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-06-08 16:01:44.283][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-06-08 16:01:44.284][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-06-08 16:01:44.285][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-06-08 16:01:44.286][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-06-08 16:01:44.287][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-06-08 16:01:44.288][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-06-08 16:01:44.289][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-06-08 16:01:44.290][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-06-08 16:01:44.291][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-06-08 16:01:44.292][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-06-08 16:01:44.293][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-06-08 16:01:44.294][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-06-08 16:01:44.295][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-06-08 16:01:44.296][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-06-08 16:01:44.297][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-06-08 16:01:44.298][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-06-08 16:01:44.299][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-06-08 16:01:44.300][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-06-08 16:01:44.301][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-06-08 16:01:44.302][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-06-08 16:01:44.303][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-06-08 16:01:44.304][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-06-08 16:01:44.305][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-06-08 16:01:44.306][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-06-08 16:01:44.306][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-06-08 16:01:44.307][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-06-08 16:01:44.308][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-06-08 16:01:44.309][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-06-08 16:01:44.311][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-06-08 16:01:44.312][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-06-08 16:01:44.313][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-06-08 16:01:44.314][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-06-08 16:01:44.315][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-08 16:01:44.316][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-08 16:01:44.316][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-06-08 16:01:44.318][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-06-08 16:01:44.318][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-06-08 16:01:44.319][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-06-08 16:01:44.320][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-06-08 16:01:44.321][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-06-08 16:01:44.322][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-06-08 16:01:44.323][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-06-08 16:01:44.324][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-06-08 16:01:44.325][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-06-08 16:01:44.326][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-06-08 16:01:44.327][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-06-08 16:01:44.328][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-06-08 16:01:44.329][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-06-08 16:01:44.330][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-06-08 16:01:44.334][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-06-08 16:01:44.336][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-06-08 16:01:44.338][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-08 16:01:44.338][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:01:44.339][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:01:44.340][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:01:44.340][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:01:44.343][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:01:44.344][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:01:44.345][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:01:44.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:01:44.346][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:01:44.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:01:44.347][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:01:44.348][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:01:44.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:01:44.349][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:01:44.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:01:44.350][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:01:44.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:01:44.352][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[2024-06-08 16:01:44.352][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:01:44.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:01:44.354][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:01:44.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:01:44.355][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:01:44.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:01:44.356][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:01:44.357][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:01:44.357][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:01:44.358][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:01:44.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:01:44.359][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:01:44.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:01:44.360][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[2024-06-08 16:01:44.361][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:01:44.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:01:44.362][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:01:44.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:01:44.363][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:01:44.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:01:44.365][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:01:44.365][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:01:44.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:01:44.366][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:01:44.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:01:44.368][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:01:44.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:01:44.369][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:01:44.370][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:01:44.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:01:44.371][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:01:44.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:01:44.372][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:01:44.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:01:44.373][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:01:44.374][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:01:44.374][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:01:44.375][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:01:44.376][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:01:44.376][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:01:44.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:01:44.378][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:01:44.378][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:01:44.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:01:44.379][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:01:44.380][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:01:44.381][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:01:44.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:01:44.382][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:01:44.383][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:01:44.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:01:44.384][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:01:44.384][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:01:44.385][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:01:44.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:01:44.386][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:01:44.387][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:01:44.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:01:44.388][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:01:44.389][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:01:44.389][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:01:44.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:01:44.391][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:01:44.391][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:01:44.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:01:44.393][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:01:44.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:01:44.394][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:01:44.394][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:01:44.395][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:01:44.396][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:01:44.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:01:44.401][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:01:44.402][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:01:44.402][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:01:44.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:01:44.404][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:01:44.404][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:01:44.405][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:01:44.405][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:01:44.406][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:01:44.407][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:01:44.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:01:44.408][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:01:44.409][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:01:44.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:01:44.410][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:01:44.410][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:01:44.411][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:01:44.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:01:44.412][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:01:44.413][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:01:44.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:01:44.414][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:01:44.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:01:44.415][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:01:44.416][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:01:44.417][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:01:44.417][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:01:44.418][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:01:44.419][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:01:44.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:01:44.420][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:01:44.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:01:44.421][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:01:44.423][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.19-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/definitions.yml".
biodb.DEBUG[2024-06-08 16:01:44.429][self$getDbsInfo()$define] Define connector expasy.enzyme.
biodb.DEBUG[2024-06-08 16:01:44.431][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-08 16:01:44.431][self$setPropertyValue] Setting property "description" to "Write here the description of this database.".
biodb.DEBUG[2024-06-08 16:01:44.432][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-08 16:01:44.433][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-08 16:01:44.434][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-08 16:01:44.434][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-08 16:01:44.435][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-06-08 16:01:44.436][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-08 16:01:44.436][self$setPropertyValue] Setting property "entry.content.type" to "txt".
biodb.DEBUG[2024-06-08 16:01:44.437][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-08 16:01:44.438][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-08 16:01:44.439][self$setPropertyValue] Setting property "name" to "Expasy ENZYME database.".
biodb.DEBUG[2024-06-08 16:01:44.439][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-08 16:01:44.440][self$setPropertyValue] Setting property "parsing.expr" to "^ID\s+([0-9.]+)$".
biodb.DEBUG[2024-06-08 16:01:44.440][self$setPropertyValue] Setting property "parsing.expr" to "^CA\s+(.+?)\.?$".
biodb.DEBUG[2024-06-08 16:01:44.440][self$setPropertyValue] Setting property "parsing.expr" to "^CF\s+(.+?)\.?$".
biodb.DEBUG[2024-06-08 16:01:44.440][self$setPropertyValue] Setting property "parsing.expr" to "^DE\s+(.+?)\.?$".
biodb.DEBUG[2024-06-08 16:01:44.441][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-06-08 16:01:44.441][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-08 16:01:44.442][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-06-08 16:01:44.443][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-08 16:01:44.443][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-08 16:01:44.444][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-08 16:01:44.445][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-08 16:01:44.446][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-08 16:01:44.446][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-08 16:01:44.447][self$setPropertyValue] Setting property "urls" to "https://enzyme.expasy.org/".
biodb.DEBUG[2024-06-08 16:01:44.448][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-08 16:01:44.448][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-08 16:01:44.449][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-06-08 16:01:44.450][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:01:44.454][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-08 16:01:44.471][super$initialize] Initialize connector expasy.enzyme.
biodb.DEBUG[2024-06-08 16:01:44.472][super$initialize] Register connector expasy.enzyme with the request scheduler
biodb.DEBUG[2024-06-08 16:01:44.475][private$bdb$getRequestScheduler()$re ...] Register connector expasy.enzyme.
biodb.DEBUG[2024-06-08 16:01:44.478][private$addConnectorRules] Create new rule for URL "enzyme.expasy.org" of connector "expasy.enzyme".
biodb.DEBUG[2024-06-08 16:01:44.481][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-08 16:01:44.481][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-08 16:01:44.482][biodb$getFactory()$createConn] Creating new connector expasy.enzyme for database class expasy.enzyme .
biodb.INFO [2024-06-08 16:01:44.489][biodb::testThat]
biodb.INFO [2024-06-08 16:01:44.490][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-06-08 16:01:44.491][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-08 16:01:44.492][biodb::testThat]
biodb.TRACE[2024-06-08 16:01:44.494][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.19-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/testref/entry-expasy.enzyme-1.1.1.1-content.txt".
biodb.DEBUG[2024-06-08 16:01:44.496][biodb$getFactory()$createEntryFromCo ...] Creating Expasy ENZYME database. entries from 1 content(s).
biodb.DEBUG[2024-06-08 16:01:44.498][biodb$getFactory()$createEntryFromCo ...] Parsing 1 Expasy ENZYME database. entries.
biodb.DEBUG[2024-06-08 16:01:44.504][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-08 16:01:44.505][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:01:44.506][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:01:44.516][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:01:44.517][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:01:44.517][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:01:44.518][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-08 16:01:44.525][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:01:44.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:01:44.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:44.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:44.552][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-08 16:01:44.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-08 16:01:44.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:44.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:44.563][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-08 16:01:44.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-08 16:01:44.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:44.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:44.566][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:01:44.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:01:44.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:44.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:44.569][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-06-08 16:01:44.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-08 16:01:44.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:44.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:44.572][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-08 16:01:44.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-08 16:01:44.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:44.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:44.575][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-08 16:01:44.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-08 16:01:44.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:44.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:44.578][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-08 16:01:44.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-08 16:01:44.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:44.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:44.581][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-06-08 16:01:44.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-08 16:01:44.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:44.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:44.595][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:01:44.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:01:44.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:44.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:44.598][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:01:44.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:01:44.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:44.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:44.623][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:01:44.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:01:44.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:44.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:44.627][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:01:44.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:01:44.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:44.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:44.629][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:01:44.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:01:44.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:44.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:44.632][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-08 16:01:44.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-08 16:01:44.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:44.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:44.635][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-08 16:01:44.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-08 16:01:44.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:44.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:44.638][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:01:44.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:01:44.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:44.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:44.641][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-08 16:01:44.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-08 16:01:44.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:44.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:44.644][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:01:44.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:01:44.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:44.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:44.673][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:01:44.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:01:44.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:44.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:44.675][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:01:44.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:01:44.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:44.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:44.678][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:01:44.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:01:44.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:44.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:44.681][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:01:44.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:01:44.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:44.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:44.684][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:01:44.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:01:44.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:44.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-08 16:01:44.687][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 1.1.1.1.
biodb.TRACE[2024-06-08 16:01:44.689][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-08 16:01:44.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-08 16:01:44.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:44.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:44.691][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-08 16:01:44.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-08 16:01:44.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:44.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:44.694][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-08 16:01:44.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-08 16:01:44.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:44.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:44.697][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-08 16:01:44.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-08 16:01:44.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:44.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:44.711][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:01:44.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:01:44.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:44.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:44.724][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-08 16:01:44.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-08 16:01:44.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:44.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:44.731][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:01:44.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:01:44.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:44.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:44.734][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:01:44.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:01:44.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:44.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:44.737][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:01:44.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:01:44.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:44.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:44.741][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:01:44.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:01:44.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:44.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:44.744][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:01:44.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:01:44.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:44.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:44.747][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:01:44.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:01:44.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:44.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:44.750][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-08 16:01:44.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-08 16:01:44.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:44.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:44.753][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-08 16:01:44.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-08 16:01:44.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:44.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:44.756][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-08 16:01:44.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-08 16:01:44.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:44.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:44.765][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:01:44.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:01:44.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:44.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:44.768][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:01:44.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:01:44.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:44.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:44.771][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:01:44.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:01:44.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:44.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:44.774][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:01:44.775][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:01:44.775][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:44.776][ef$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:44.777][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:01:44.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:01:44.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:44.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:44.787][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:01:44.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:01:44.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:44.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:44.794][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:01:44.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:01:44.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:44.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:44.797][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:01:44.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:01:44.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:44.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:44.800][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:01:44.801][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:01:44.802][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:44.803][ef$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:44.803][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:01:44.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:01:44.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:44.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:44.813][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-08 16:01:44.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-08 16:01:44.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:44.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:44.816][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-08 16:01:44.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-08 16:01:44.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:44.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:44.819][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-08 16:01:44.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-08 16:01:44.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:44.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:44.822][ef$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-08 16:01:44.823][ef$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-08 16:01:44.824][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:44.825][ef$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:44.825][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-08 16:01:44.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-08 16:01:44.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:44.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:44.836][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-08 16:01:44.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-08 16:01:44.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:44.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:44.839][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-08 16:01:44.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-08 16:01:44.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:44.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:44.842][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-08 16:01:44.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-08 16:01:44.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:44.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:44.845][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-08 16:01:44.846][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-08 16:01:44.847][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:44.847][ef$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:44.848][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-08 16:01:44.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-08 16:01:44.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:44.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:44.858][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:01:44.858][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:01:44.859][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:44.860][ef$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:44.864][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-08 16:01:44.865][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-08 16:01:44.865][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:44.866][ef$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:44.870][ef$get] Asked field names are: cofactor.
biodb.TRACE[2024-06-08 16:01:44.871][ef$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-08 16:01:44.872][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:44.872][ef$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:44.876][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:01:44.877][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:01:44.878][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:44.879][ef$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:44.891][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.19-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/testref/entry-expasy.enzyme-1.1.1.54-content.txt".
biodb.DEBUG[2024-06-08 16:01:44.920][biodb$getFactory()$createEntryFromCo ...] Creating Expasy ENZYME database. entries from 1 content(s).
biodb.DEBUG[2024-06-08 16:01:44.921][biodb$getFactory()$createEntryFromCo ...] Parsing 1 Expasy ENZYME database. entries.
biodb.DEBUG[2024-06-08 16:01:44.922][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-08 16:01:44.923][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:01:44.923][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:01:44.927][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:01:44.928][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:01:44.929][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:01:44.929][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-08 16:01:44.931][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:01:44.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:01:44.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:44.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:44.934][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-08 16:01:44.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-08 16:01:44.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:44.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:44.937][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:01:44.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:01:44.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:44.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:44.940][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-06-08 16:01:44.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-08 16:01:44.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:44.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:44.943][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-08 16:01:44.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-08 16:01:44.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:44.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:44.946][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-08 16:01:44.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-08 16:01:44.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:44.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:44.949][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:01:44.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:01:44.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:44.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:44.952][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-08 16:01:44.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-08 16:01:44.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:44.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:44.955][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:01:44.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:01:44.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:44.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:44.958][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:01:44.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:01:44.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:44.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:44.961][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:01:44.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:01:44.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:44.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:44.964][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:01:44.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:01:44.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:44.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:44.967][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:01:44.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:01:44.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:44.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:44.970][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:01:44.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:01:44.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:44.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-08 16:01:44.973][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 1.1.1.54.
biodb.TRACE[2024-06-08 16:01:44.988][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-08 16:01:44.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-08 16:01:44.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:44.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:44.991][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-08 16:01:44.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-08 16:01:44.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:44.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:44.994][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-08 16:01:44.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-08 16:01:44.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:44.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:44.996][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-08 16:01:44.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-08 16:01:44.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:44.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:45.000][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:01:45.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:01:45.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:45.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:45.007][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-08 16:01:45.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-08 16:01:45.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:45.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:45.013][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:01:45.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:01:45.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:45.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:45.016][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:01:45.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:01:45.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:45.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:45.023][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:01:45.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:01:45.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:45.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:45.027][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:01:45.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:01:45.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:45.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:45.030][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:01:45.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:01:45.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:45.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:45.033][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:01:45.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:01:45.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:45.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:45.036][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-08 16:01:45.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-08 16:01:45.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:45.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:45.039][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-08 16:01:45.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-08 16:01:45.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:45.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:45.042][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-08 16:01:45.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-08 16:01:45.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:45.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:45.057][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:01:45.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:01:45.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:45.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:45.060][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:01:45.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:01:45.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:45.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:45.063][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:01:45.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:01:45.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:45.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:45.066][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:01:45.067][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:01:45.068][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:45.069][ef$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:45.069][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:01:45.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:01:45.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:45.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:45.078][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:01:45.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:01:45.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:45.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:45.081][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:01:45.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:01:45.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:45.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:45.084][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:01:45.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:01:45.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:45.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:45.087][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:01:45.088][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:01:45.089][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:45.089][ef$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:45.090][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:01:45.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:01:45.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:45.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:45.100][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-08 16:01:45.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-08 16:01:45.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:45.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:45.103][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-08 16:01:45.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-08 16:01:45.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:45.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:45.106][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-08 16:01:45.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-08 16:01:45.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:45.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:45.108][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-08 16:01:45.109][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-08 16:01:45.110][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:45.111][ef$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:45.112][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-08 16:01:45.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-08 16:01:45.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:45.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:45.122][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:01:45.123][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:01:45.124][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:45.124][ef$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:45.129][ef$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-08 16:01:45.129][ef$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-08 16:01:45.130][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:45.131][ef$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:01:45.135][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:01:45.136][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:01:45.136][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:01:45.141][ef$get] fields variable is a list.
biodb.INFO [2024-06-08 16:01:45.148][biodb::testThat]
biodb.INFO [2024-06-08 16:01:45.149][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-06-08 16:01:45.149][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-08 16:01:45.150][biodb::testThat]
biodb.DEBUG[2024-06-08 16:01:45.152][private$loadEntries] Creating entries from ids [2]: "1.1.1.1, 1.1.1.54".
biodb.DEBUG[2024-06-08 16:01:45.157][conn$getEntryContent] Get Expasy ENZYME database. entry content(s) for 2 id(s)...
biodb.TRACE[2024-06-08 16:01:45.162][cch$loadFileContent] Trying to load 2 files from cache: [2]: "1.1.1.1, 1.1.1.54".
biodb.INFO [2024-06-08 16:01:45.163][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280" for "expasy.enzyme-b59b84d962b6741050ba8f70ff4db280".
biodb.TRACE[2024-06-08 16:01:45.164][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2024-06-08 16:01:45.165][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-08 16:01:45.166][conn$getEntryContent] 0 Expasy ENZYME database. entry content(s) loaded from cache.
biodb.DEBUG[2024-06-08 16:01:45.166][conn$getEntryContent] 2 entry content(s) need to be fetched from Expasy ENZYME database. database "https://enzyme.expasy.org/".
biodb.DEBUG[2024-06-08 16:01:45.167][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-08 16:01:45.168][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-08 16:01:45.172][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-08 16:01:45.172][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:01:45.173][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:01:45.177][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:01:45.178][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:01:45.179][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:01:45.179][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:01:45.180][scheduler$sendRequest] Getting content of get URL request "https://enzyme.expasy.org/EC/1.1.1.1.txt".
biodb.DEBUG[2024-06-08 16:01:45.195][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-08 16:01:45.196][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-08 16:01:45.197][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/EC/1.1.1.1.txt".
biodb.TRACE[2024-06-08 16:02:45.387][doesRCurlRequestUrlExist] According to RCurl, URL https://enzyme.expasy.org/EC/1.1.1.1.txt does not exist.
biodb.TRACE[2024-06-08 16:02:45.388][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-06-08 16:02:45.389][getUrlRequestResult] URL "https://enzyme.expasy.org/EC/1.1.1.1.txt" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-06-08 16:02:45.390][getBaseUrlRequestResult] Using base::url() for sending request (https://enzyme.expasy.org/EC/1.1.1.1.txt).
biodb.DEBUG[2024-06-08 16:03:35.216][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-08 16:03:35.217][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a52675cfd2f0c2b41556caa64d9341e3.content"
biodb.TRACE[2024-06-08 16:03:35.228][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a52675cfd2f0c2b41556caa64d9341e3.request"
biodb.DEBUG[2024-06-08 16:03:35.229][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-08 16:03:35.230][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:03:35.231][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:03:35.235][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:03:35.236][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:03:35.236][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:03:35.237][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:03:35.251][scheduler$sendRequest] Getting content of get URL request "https://enzyme.expasy.org/EC/1.1.1.54.txt".
biodb.DEBUG[2024-06-08 16:03:35.262][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-08 16:03:35.262][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-08 16:03:35.277][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/EC/1.1.1.54.txt".
biodb.TRACE[2024-06-08 16:03:57.115][getRCurlRequestResult] Using RCurl package for sending request (https://enzyme.expasy.org/EC/1.1.1.54.txt).
biodb.DEBUG[2024-06-08 16:04:04.605][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-08 16:04:04.607][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a9b93566a091cbe35a06e4b3871f95c9.content"
biodb.TRACE[2024-06-08 16:04:04.610][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a9b93566a091cbe35a06e4b3871f95c9.request"
biodb.TRACE[2024-06-08 16:04:04.612][private$doSaveContentToFile] Saving to cache [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/1.1.1.1.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/1.1.1.54.txt"
biodb.DEBUG[2024-06-08 16:04:04.613][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-08 16:04:04.614][self$createEntryFromContent] Creating Expasy ENZYME database. entries from 2 content(s).
biodb.DEBUG[2024-06-08 16:04:04.615][self$createEntryFromContent] Parsing 2 Expasy ENZYME database. entries.
biodb.DEBUG[2024-06-08 16:04:04.616][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-08 16:04:04.617][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:04:04.618][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:04:04.622][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:04:04.623][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:04:04.623][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:04:04.624][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-08 16:04:04.626][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:04:04.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:04:04.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:04.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:04:04.629][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-08 16:04:04.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-08 16:04:04.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:04.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:04:04.633][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:04:04.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:04:04.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:04.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:04:04.636][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-06-08 16:04:04.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-08 16:04:04.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:04.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:04:04.639][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:04:04.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:04:04.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:04.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:04:04.642][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:04:04.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:04:04.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:04.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:04:04.645][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:04:04.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:04:04.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:04.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:04:04.648][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:04:04.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:04:04.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:04.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:04:04.651][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:04:04.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:04:04.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:04.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:04:04.654][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-08 16:04:04.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-08 16:04:04.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:04.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:04:04.657][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-08 16:04:04.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-08 16:04:04.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:04.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:04:04.660][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:04:04.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:04:04.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:04.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:04:04.663][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-08 16:04:04.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-08 16:04:04.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:04.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:04:04.666][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:04:04.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:04:04.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:04.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:04:04.669][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:04:04.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:04:04.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:04.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:04:04.671][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:04:04.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:04:04.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:04.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-08 16:04:04.675][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-08 16:04:04.675][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:04:04.676][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:04:04.680][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:04:04.681][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:04:04.688][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:04:04.689][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-08 16:04:04.690][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:04:04.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:04:04.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:04.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:04:04.693][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity.
biodb.TRACE[2024-06-08 16:04:04.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity.
biodb.TRACE[2024-06-08 16:04:04.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:04.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:04:04.697][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:04:04.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:04:04.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:04.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:04:04.700][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR.
biodb.TRACE[2024-06-08 16:04:04.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor.
biodb.TRACE[2024-06-08 16:04:04.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:04.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:04:04.703][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-08 16:04:04.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-08 16:04:04.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:04.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:04:04.706][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-08 16:04:04.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-08 16:04:04.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:04.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:04:04.709][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:04:04.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:04:04.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:04.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:04:04.712][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id.
biodb.TRACE[2024-06-08 16:04:04.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id.
biodb.TRACE[2024-06-08 16:04:04.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:04.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:04:04.715][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:04:04.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:04:04.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:04.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:04:04.718][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:04:04.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:04:04.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:04.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:04:04.721][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:04:04.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:04:04.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:04.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:04:04.724][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:04:04.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:04:04.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:04.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:04:04.727][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:04:04.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:04:04.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:04.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:04:04.730][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:04:04.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:04:04.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:04.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:04:04.733][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:04:04.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:04:04.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:04.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:04:04.737][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:04:04.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:04:04.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:04.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:04:04.740][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:04:04.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:04:04.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:04.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-08 16:04:04.743][self$createEntryFromContent] Accession numbers: 1.1.1.1, 1.1.1.54.
biodb.TRACE[2024-06-08 16:04:04.744][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-06-08 16:04:04.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-06-08 16:04:04.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:04.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:04:04.747][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-06-08 16:04:04.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-06-08 16:04:04.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:04.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:04:04.750][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-06-08 16:04:04.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-06-08 16:04:04.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:04.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:04:04.757][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-06-08 16:04:04.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-06-08 16:04:04.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:04.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:04:04.760][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-06-08 16:04:04.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-06-08 16:04:04.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:04.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:04:04.763][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-06-08 16:04:04.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-06-08 16:04:04.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:04.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-08 16:04:04.772][biodb::testThat]
biodb.INFO [2024-06-08 16:04:04.773][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-06-08 16:04:04.773][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-08 16:04:04.774][biodb::testThat]
biodb.TRACE[2024-06-08 16:04:04.776][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:04:04.777][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:04:04.778][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:04.778][ef$get] fields variable is a list.
biodb.DEBUG[2024-06-08 16:04:04.783][function(conn, opt)] Testing searchForEntries() with entry "1.1.1.1" and field "name".
biodb.TRACE[2024-06-08 16:04:04.803][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:04:04.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:04:04.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:04.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:04:04.806][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:04:04.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:04:04.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:04.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:04:04.809][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:04:04.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:04:04.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:04.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-08 16:04:04.814][function(conn, opt)] With value "alcohol dehydrogenase".
biodb.DEBUG[2024-06-08 16:04:04.815][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://enzyme.expasy.org/enzyme-byname.html?alcohol dehydrogenase".
biodb.DEBUG[2024-06-08 16:04:04.817][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-08 16:04:04.818][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-08 16:04:04.819][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase".
biodb.TRACE[2024-06-08 16:04:11.377][getRCurlRequestResult] Using RCurl package for sending request (https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase).
biodb.DEBUG[2024-06-08 16:04:13.611][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-08 16:04:13.613][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.content"
biodb.TRACE[2024-06-08 16:04:13.616][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.request"
biodb.DEBUG[2024-06-08 16:04:13.620][function(conn, opt)] With found IDs [1]: "1.1.1.1".
biodb.INFO [2024-06-08 16:04:13.640][biodb::testThat]
biodb.INFO [2024-06-08 16:04:13.641][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-06-08 16:04:13.641][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-08 16:04:13.642][biodb::testThat]
biodb.TRACE[2024-06-08 16:04:13.663][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:04:13.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:04:13.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:13.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:04:13.666][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:04:13.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:04:13.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:13.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:04:13.669][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:04:13.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:04:13.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:13.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-08 16:04:13.698][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://enzyme.expasy.org/enzyme-byname.html?alcohol dehydrogenase".
biodb.DEBUG[2024-06-08 16:04:13.701][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-08 16:04:13.712][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f603fa2a57aec59588edc37541c6f6d5".
biodb.TRACE[2024-06-08 16:04:13.714][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-08 16:04:13.715][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.content".
biodb.INFO [2024-06-08 16:04:13.734][biodb::testThat]
biodb.INFO [2024-06-08 16:04:13.735][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-06-08 16:04:13.736][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-08 16:04:13.737][biodb::testThat]
biodb.TRACE[2024-06-08 16:04:13.745][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-08 16:04:13.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-08 16:04:13.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:13.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:04:13.748][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-08 16:04:13.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-08 16:04:13.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:13.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:04:13.751][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-08 16:04:13.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-08 16:04:13.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:13.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:04:13.753][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-08 16:04:13.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-08 16:04:13.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:13.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:04:13.783][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-08 16:04:13.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-08 16:04:13.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:13.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:04:13.786][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-08 16:04:13.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-08 16:04:13.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:13.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:04:13.789][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-08 16:04:13.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-08 16:04:13.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:13.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:04:13.792][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-08 16:04:13.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-08 16:04:13.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:04:13.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-08 16:04:13.800][biodb::testThat]
biodb.INFO [2024-06-08 16:04:13.801][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-06-08 16:04:13.801][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-08 16:04:13.802][biodb::testThat]
biodb.INFO [2024-06-08 16:04:13.813][biodb::testThat]
biodb.INFO [2024-06-08 16:04:13.814][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-06-08 16:04:13.815][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-08 16:04:13.815][biodb::testThat]
biodb.INFO [2024-06-08 16:04:13.822][biodb::testThat]
biodb.INFO [2024-06-08 16:04:13.823][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-06-08 16:04:13.824][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-08 16:04:13.824][biodb::testThat]
biodb.DEBUG[2024-06-08 16:04:13.835][function(conn, opt)] Trying to download "https://enzyme.expasy.org/cgi-bin/enzyme/enzyme-search-ec?field1=1&field2=1&field3=1&field4=1".
biodb.DEBUG[2024-06-08 16:04:16.556][getUrlContent] Use RCurl for downloading content of URL https://enzyme.expasy.org/cgi-bin/enzyme/enzyme-search-ec?field1=1&field2=1&field3=1&field4=1.
biodb.INFO [2024-06-08 16:04:34.472][biodb::testThat]
biodb.INFO [2024-06-08 16:04:34.473][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-06-08 16:04:34.473][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-08 16:04:34.474][biodb::testThat]
biodb.DEBUG[2024-06-08 16:05:17.010][getUrlContent] Use base::url() for downloading content of URL https://enzyme.expasy.org/images/1.1.1.1/image.png.
biodb.TRACE[2024-06-08 16:05:53.311][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:05:53.312][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:05:53.313][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:53.313][ef$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:05:53.314][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:05:53.315][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:05:53.316][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:05:53.316][ef$get] fields variable is a list.
biodb.INFO [2024-06-08 16:05:53.317][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-06-08 16:05:53.318][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector expasy.enzyme from the request scheduler
biodb.INFO [2024-06-08 16:05:53.319][self$deleteConn] Connector "expasy.enzyme" deleted.
biodb.DEBUG[2024-06-08 16:05:53.320][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-06-08 16:05:53.320][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:05:53.321][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:05:53.322][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:53.322][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:53.323][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:53.324][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-06-08 16:05:53.331][biodb::testContext]
biodb.INFO [2024-06-08 16:05:53.332][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-08 16:05:53.333][biodb::testContext] Test context - Example long tests
biodb.INFO [2024-06-08 16:05:53.334][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-08 16:05:53.334][biodb::testContext]
biodb.INFO [2024-06-08 16:05:53.336][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-06-08 16:05:53.337][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-06-08 16:05:53.340][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-08 16:05:53.341][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-06-08 16:05:53.342][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-06-08 16:05:53.343][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:53.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:53.344][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:53.345][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-06-08 16:05:53.345][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-06-08 16:05:53.346][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:53.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:53.348][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:53.348][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-06-08 16:05:53.349][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-06-08 16:05:53.350][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:53.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:53.351][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:53.352][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-06-08 16:05:53.353][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-06-08 16:05:53.353][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-06-08 16:05:53.354][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:53.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:53.355][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:53.356][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-06-08 16:05:53.357][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-06-08 16:05:53.358][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-06-08 16:05:53.358][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:53.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:53.360][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[2024-06-08 16:05:53.361][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-06-08 16:05:53.361][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-06-08 16:05:53.362][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:53.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:53.364][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:53.364][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-06-08 16:05:53.365][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-06-08 16:05:53.366][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-06-08 16:05:53.367][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:53.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:53.368][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:53.369][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-06-08 16:05:53.369][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-06-08 16:05:53.370][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:53.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:53.371][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:53.372][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-06-08 16:05:53.373][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-06-08 16:05:53.374][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-06-08 16:05:53.375][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:53.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:53.376][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:53.377][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-06-08 16:05:53.377][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-06-08 16:05:53.378][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-06-08 16:05:53.379][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-06-08 16:05:53.380][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-06-08 16:05:53.380][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-06-08 16:05:53.381][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:53.382][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:53.383][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:53.383][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-06-08 16:05:53.384][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-06-08 16:05:53.385][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:53.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:53.390][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:53.391][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-06-08 16:05:53.392][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-06-08 16:05:53.393][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:53.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:53.394][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:53.395][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-06-08 16:05:53.396][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-06-08 16:05:53.396][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:53.397][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:53.397][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:53.398][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-06-08 16:05:53.399][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-06-08 16:05:53.400][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:53.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:53.401][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:53.402][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-06-08 16:05:53.402][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-06-08 16:05:53.403][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:53.404][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:53.404][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:53.405][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-06-08 16:05:53.406][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-06-08 16:05:53.421][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-06-08 16:05:53.422][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:53.423][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:53.423][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:53.424][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-06-08 16:05:53.425][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-06-08 16:05:53.426][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-06-08 16:05:53.426][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:53.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:53.428][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:53.429][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-06-08 16:05:53.430][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-08 16:05:53.431][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-06-08 16:05:53.432][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-08 16:05:53.432][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-08 16:05:53.433][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-08 16:05:53.434][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-08 16:05:53.435][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-08 16:05:53.436][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-08 16:05:53.436][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-08 16:05:53.437][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-08 16:05:53.438][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-08 16:05:53.439][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-06-08 16:05:53.439][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-08 16:05:53.440][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:05:53.441][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-08 16:05:53.442][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-08 16:05:53.442][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-08 16:05:53.442][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-08 16:05:53.442][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-08 16:05:53.442][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-08 16:05:53.443][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-08 16:05:53.443][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-08 16:05:53.444][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-08 16:05:53.462][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-08 16:05:53.463][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-08 16:05:53.464][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-08 16:05:53.465][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-08 16:05:53.465][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:05:53.466][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-08 16:05:53.467][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-08 16:05:53.467][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-08 16:05:53.468][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:05:53.469][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-06-08 16:05:53.470][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-08 16:05:53.471][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-06-08 16:05:53.472][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-08 16:05:53.473][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-08 16:05:53.474][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-08 16:05:53.476][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-08 16:05:53.479][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-08 16:05:53.481][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-08 16:05:53.481][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-08 16:05:53.482][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-08 16:05:53.483][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-08 16:05:53.484][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-06-08 16:05:53.484][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-08 16:05:53.485][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:05:53.486][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-08 16:05:53.487][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-08 16:05:53.487][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-08 16:05:53.487][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-08 16:05:53.487][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-08 16:05:53.487][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-08 16:05:53.488][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-08 16:05:53.488][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-08 16:05:53.489][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-08 16:05:53.490][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-08 16:05:53.490][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-08 16:05:53.491][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-08 16:05:53.492][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-08 16:05:53.493][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:05:53.493][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-08 16:05:53.494][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-08 16:05:53.495][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-08 16:05:53.496][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:05:53.496][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-06-08 16:05:53.498][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-08 16:05:53.499][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-06-08 16:05:53.499][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-08 16:05:53.500][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-08 16:05:53.501][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-08 16:05:53.502][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-08 16:05:53.502][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-08 16:05:53.503][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-08 16:05:53.504][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-08 16:05:53.505][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-08 16:05:53.505][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-08 16:05:53.506][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-06-08 16:05:53.507][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-08 16:05:53.508][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:05:53.509][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-08 16:05:53.513][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:05:53.514][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-08 16:05:53.515][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-08 16:05:53.515][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-08 16:05:53.516][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-08 16:05:53.517][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-08 16:05:53.517][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-08 16:05:53.518][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-08 16:05:53.519][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:05:53.520][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-08 16:05:53.520][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-08 16:05:53.521][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-08 16:05:53.522][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:05:53.523][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-06-08 16:05:53.524][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-08 16:05:53.525][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-06-08 16:05:53.525][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-08 16:05:53.526][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-08 16:05:53.527][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-08 16:05:53.528][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-08 16:05:53.528][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-08 16:05:53.529][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-08 16:05:53.530][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-08 16:05:53.531][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-08 16:05:53.531][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-08 16:05:53.532][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-06-08 16:05:53.533][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-08 16:05:53.534][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:05:53.534][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-08 16:05:53.535][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:05:53.536][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-08 16:05:53.537][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-08 16:05:53.537][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-08 16:05:53.538][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-08 16:05:53.539][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-08 16:05:53.540][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-08 16:05:53.541][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-08 16:05:53.541][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:05:53.542][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-08 16:05:53.543][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-08 16:05:53.543][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-08 16:05:53.544][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:05:53.545][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-08 16:05:53.546][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:53.547][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:53.547][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:53.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:53.549][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:53.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:53.550][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:53.551][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:53.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:53.552][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:53.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:53.553][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:53.554][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:53.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:53.555][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:53.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:53.557][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:53.557][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:53.558][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:53.559][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:53.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:53.560][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:53.561][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:53.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:53.562][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:53.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:53.564][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[2024-06-08 16:05:53.564][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:53.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:53.566][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:53.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:53.567][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:53.568][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:53.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:53.569][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:53.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:53.570][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[2024-06-08 16:05:53.571][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:53.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:53.572][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:53.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:53.574][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:53.574][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:53.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:53.576][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:53.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:53.577][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:53.578][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:53.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:53.579][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:53.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:53.580][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:53.581][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:53.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:53.582][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:53.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:53.584][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:53.584][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:53.585][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:53.586][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:53.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:53.587][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:53.588][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:53.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:53.589][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:53.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:53.590][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:53.591][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:53.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:53.592][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:53.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:53.598][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:53.598][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:53.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:53.600][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:53.600][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:53.601][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:53.602][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:53.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:53.603][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:53.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:53.604][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:53.605][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:53.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:53.606][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:53.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:53.607][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:53.608][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-06-08 16:05:53.609][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-06-08 16:05:53.610][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-06-08 16:05:53.611][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-06-08 16:05:53.612][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-08 16:05:53.613][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-08 16:05:53.614][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-06-08 16:05:53.615][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-06-08 16:05:53.616][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-08 16:05:53.617][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-08 16:05:53.619][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-08 16:05:53.620][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-06-08 16:05:53.621][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-06-08 16:05:53.622][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-06-08 16:05:53.623][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-06-08 16:05:53.624][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-08 16:05:53.625][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-06-08 16:05:53.626][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-06-08 16:05:53.627][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-08 16:05:53.628][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-06-08 16:05:53.629][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-06-08 16:05:53.630][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-06-08 16:05:53.631][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-06-08 16:05:53.632][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-06-08 16:05:53.633][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-06-08 16:05:53.634][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-06-08 16:05:53.635][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-06-08 16:05:53.636][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-06-08 16:05:53.637][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-06-08 16:05:53.638][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-06-08 16:05:53.639][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-06-08 16:05:53.640][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-06-08 16:05:53.641][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-06-08 16:05:53.642][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-06-08 16:05:53.643][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-06-08 16:05:53.644][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-06-08 16:05:53.646][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-06-08 16:05:53.647][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-06-08 16:05:53.648][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-06-08 16:05:53.648][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-06-08 16:05:53.649][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-06-08 16:05:53.651][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-06-08 16:05:53.652][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-06-08 16:05:53.653][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-06-08 16:05:53.654][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-06-08 16:05:53.655][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-06-08 16:05:53.656][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-06-08 16:05:53.657][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-06-08 16:05:53.658][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-06-08 16:05:53.659][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-06-08 16:05:53.660][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-06-08 16:05:53.661][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-06-08 16:05:53.662][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-06-08 16:05:53.663][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-06-08 16:05:53.664][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-06-08 16:05:53.665][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-06-08 16:05:53.666][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-06-08 16:05:53.667][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-06-08 16:05:53.668][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-06-08 16:05:53.670][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-06-08 16:05:53.671][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-06-08 16:05:53.672][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-06-08 16:05:53.673][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-06-08 16:05:53.674][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-06-08 16:05:53.679][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-06-08 16:05:53.680][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-06-08 16:05:53.681][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-08 16:05:53.682][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-08 16:05:53.683][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-06-08 16:05:53.684][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-06-08 16:05:53.686][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-06-08 16:05:53.687][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-06-08 16:05:53.688][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-06-08 16:05:53.689][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-06-08 16:05:53.690][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-06-08 16:05:53.691][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-06-08 16:05:53.692][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-06-08 16:05:53.693][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-06-08 16:05:53.694][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-06-08 16:05:53.695][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-06-08 16:05:53.696][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-06-08 16:05:53.697][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-06-08 16:05:53.698][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-06-08 16:05:53.699][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-06-08 16:05:53.700][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-06-08 16:05:53.701][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-08 16:05:53.702][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:53.702][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:53.703][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:53.704][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:53.704][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:53.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:05:53.706][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:05:53.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:53.707][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:53.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:53.708][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:53.709][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:53.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:05:53.710][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:05:53.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:53.712][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:53.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:53.713][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:53.714][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:53.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:05:53.715][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:05:53.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:53.716][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:53.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:53.718][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:53.718][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:53.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:05:53.719][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:05:53.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:53.721][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:53.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:53.722][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:53.723][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:53.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:05:53.724][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:05:53.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:53.725][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:53.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:53.727][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:53.727][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:53.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:05:53.729][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:05:53.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:53.730][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:53.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:53.732][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[2024-06-08 16:05:53.732][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:53.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:05:53.734][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:05:53.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:53.735][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:53.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:53.736][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:53.737][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:53.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:05:53.738][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:05:53.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:53.740][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:53.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:53.741][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:53.742][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:53.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:05:53.743][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:05:53.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:53.744][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:53.745][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:53.746][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:53.746][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:53.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:05:53.748][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:05:53.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:53.749][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:53.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:53.750][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:53.751][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:53.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:05:53.752][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:05:53.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:53.754][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:53.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:53.755][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:53.756][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:53.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:05:53.761][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:05:53.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:53.762][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:53.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:53.764][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:53.764][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:53.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:05:53.766][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:05:53.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:53.767][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:53.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:53.768][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:53.769][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:53.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:05:53.770][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:05:53.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:53.771][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:53.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:53.773][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:53.773][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:53.774][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:05:53.774][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:05:53.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:53.776][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:53.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:53.777][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:53.778][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:53.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:05:53.779][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:05:53.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:53.780][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:53.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:53.781][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:05:53.782][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:05:53.783][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:05:53.783][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:05:53.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:53.785][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:53.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:53.786][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[2024-06-08 16:05:53.788][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.19-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/definitions.yml".
biodb.DEBUG[2024-06-08 16:05:53.789][self$getDbsInfo()$define] Define connector expasy.enzyme.
biodb.DEBUG[2024-06-08 16:05:53.790][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-08 16:05:53.791][self$setPropertyValue] Setting property "description" to "Write here the description of this database.".
biodb.DEBUG[2024-06-08 16:05:53.791][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-08 16:05:53.792][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-08 16:05:53.793][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-08 16:05:53.794][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-08 16:05:53.794][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-06-08 16:05:53.795][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-08 16:05:53.796][self$setPropertyValue] Setting property "entry.content.type" to "txt".
biodb.DEBUG[2024-06-08 16:05:53.797][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-08 16:05:53.797][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-08 16:05:53.798][self$setPropertyValue] Setting property "name" to "Expasy ENZYME database.".
biodb.DEBUG[2024-06-08 16:05:53.799][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-08 16:05:53.800][self$setPropertyValue] Setting property "parsing.expr" to "^ID\s+([0-9.]+)$".
biodb.DEBUG[2024-06-08 16:05:53.800][self$setPropertyValue] Setting property "parsing.expr" to "^CA\s+(.+?)\.?$".
biodb.DEBUG[2024-06-08 16:05:53.800][self$setPropertyValue] Setting property "parsing.expr" to "^CF\s+(.+?)\.?$".
biodb.DEBUG[2024-06-08 16:05:53.800][self$setPropertyValue] Setting property "parsing.expr" to "^DE\s+(.+?)\.?$".
biodb.DEBUG[2024-06-08 16:05:53.800][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-06-08 16:05:53.801][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-08 16:05:53.802][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-06-08 16:05:53.803][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-08 16:05:53.803][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-08 16:05:53.804][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-08 16:05:53.805][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-08 16:05:53.805][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-08 16:05:53.806][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-08 16:05:53.807][self$setPropertyValue] Setting property "urls" to "https://enzyme.expasy.org/".
biodb.DEBUG[2024-06-08 16:05:53.807][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-08 16:05:53.808][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-08 16:05:53.809][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-06-08 16:05:53.810][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:05:53.810][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-08 16:05:53.813][super$initialize] Initialize connector expasy.enzyme.
biodb.DEBUG[2024-06-08 16:05:53.814][super$initialize] Register connector expasy.enzyme with the request scheduler
biodb.DEBUG[2024-06-08 16:05:53.815][private$bdb$getRequestScheduler()$re ...] Register connector expasy.enzyme.
biodb.DEBUG[2024-06-08 16:05:53.816][private$addConnectorRules] Create new rule for URL "enzyme.expasy.org" of connector "expasy.enzyme".
biodb.DEBUG[2024-06-08 16:05:53.817][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-08 16:05:53.817][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-08 16:05:53.818][biodb$getFactory()$createConn] Creating new connector expasy.enzyme for database class expasy.enzyme .
biodb.INFO [2024-06-08 16:05:53.819][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-06-08 16:05:53.820][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector expasy.enzyme from the request scheduler
biodb.INFO [2024-06-08 16:05:53.820][self$deleteConn] Connector "expasy.enzyme" deleted.
biodb.DEBUG[2024-06-08 16:05:53.821][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-06-08 16:05:53.822][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:05:53.822][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:05:53.823][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:05:53.824][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:05:53.824][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:05:53.825][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 85 ]

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

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

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbExpasy_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc-longtests/meat/biodbExpasy.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘biodbExpasy/DESCRIPTION’ ... OK
* this is package ‘biodbExpasy’ version ‘1.8.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbExpasy’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... SKIPPED
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘longtests/testthat.R’ failed.
Last 13 lines of output:
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_long_100_generic.R:37:1'): The entry image URL can be downloaded. ──
  Error in `charToRaw(content)`: argument must be a character vector of length 1
  Backtrace:
      ▆
   1. ├─base::do.call(fct, params)
   2. └─biodb (local) `<fn>`(conn = `<ExpsyEnC>`, opt = `<named list>`)
   3.   └─biodb:::getUrlContent(url, binary = TRUE)
   4.     └─biodb:::getBaseUrlContent(u, binary = binary)
   5.       └─base::charToRaw(content)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 85 ]
  Error: Test failures
  Execution halted
* DONE

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

Installation output

biodbExpasy.Rcheck/00install.out

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