Back to Long Tests report for BioC 3.15

This page was generated on 2022-10-15 21:00:02 -0400 (Sat, 15 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4383
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CHECK results for biodbNci on nebbiolo1


To the developers/maintainers of the biodbNci package:
Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 12/26HostnameOS / ArchCHECK
biodbNci 1.0.0  (landing page)
Pierrick Roger
Snapshot Date: 2022-10-15 06:55:01 -0400 (Sat, 15 Oct 2022)
git_url: https://git.bioconductor.org/packages/biodbNci
git_branch: RELEASE_3_15
git_last_commit: 538228c
git_last_commit_date: 2022-04-26 12:21:57 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK  

Summary

Package: biodbNci
Version: 1.0.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNci_1.0.0.tar.gz
StartedAt: 2022-10-15 08:08:28 -0400 (Sat, 15 Oct 2022)
EndedAt: 2022-10-15 08:19:00 -0400 (Sat, 15 Oct 2022)
EllapsedTime: 632.4 seconds
RetCode: 0
Status:   OK  
CheckDir: biodbNci.Rcheck
Warnings: 0

Tests output

biodbNci.Rcheck/tests/testthat.Rout


R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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

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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbNci)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbNci")
biodb.INFO [2022-10-15 08:09:16.498][biodb::testContext]
biodb.INFO [2022-10-15 08:09:16.500][biodb::testContext] ********************************************************************************
biodb.INFO [2022-10-15 08:09:16.500][biodb::testContext] Test context - Generic long tests
biodb.INFO [2022-10-15 08:09:16.510][biodb::testContext] ********************************************************************************
biodb.INFO [2022-10-15 08:09:16.511][biodb::testContext]
biodb.INFO [2022-10-15 08:09:16.522][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.4.2.
biodb.DEBUG[2022-10-15 08:09:16.523][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.15-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2022-10-15 08:09:16.528][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-10-15 08:09:16.529][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2022-10-15 08:09:16.530][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2022-10-15 08:09:16.531][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:09:16.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:09:16.532][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:09:16.533][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2022-10-15 08:09:16.545][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2022-10-15 08:09:16.545][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:09:16.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:09:16.547][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[2022-10-15 08:09:16.547][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2022-10-15 08:09:16.548][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2022-10-15 08:09:16.549][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:09:16.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:09:16.550][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:09:16.551][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2022-10-15 08:09:16.551][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2022-10-15 08:09:16.552][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2022-10-15 08:09:16.553][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:09:16.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:09:16.554][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:09:16.555][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2022-10-15 08:09:16.555][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2022-10-15 08:09:16.556][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2022-10-15 08:09:16.557][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:09:16.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:09:16.558][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:09:16.559][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2022-10-15 08:09:16.560][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2022-10-15 08:09:16.560][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:09:16.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:09:16.561][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:09:16.562][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2022-10-15 08:09:16.563][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2022-10-15 08:09:16.564][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2022-10-15 08:09:16.564][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:09:16.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:09:16.566][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:09:16.566][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2022-10-15 08:09:16.567][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2022-10-15 08:09:16.568][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:09:16.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:09:16.569][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:09:16.570][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2022-10-15 08:09:16.570][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2022-10-15 08:09:16.571][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2022-10-15 08:09:16.572][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:09:16.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:09:16.573][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:09:16.574][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2022-10-15 08:09:16.575][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2022-10-15 08:09:16.575][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2022-10-15 08:09:16.576][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2022-10-15 08:09:16.577][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2022-10-15 08:09:16.577][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2022-10-15 08:09:16.578][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:09:16.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:09:16.579][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:09:16.580][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2022-10-15 08:09:16.581][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2022-10-15 08:09:16.581][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:09:16.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:09:16.583][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:09:16.583][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2022-10-15 08:09:16.584][self$set] Set key entries.sep to "|".
biodb.DEBUG[2022-10-15 08:09:16.585][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:09:16.585][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:09:16.586][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:09:16.587][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2022-10-15 08:09:16.587][self$set] Set key offline to FALSE.
biodb.DEBUG[2022-10-15 08:09:16.588][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:09:16.589][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:09:16.589][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:09:16.590][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2022-10-15 08:09:16.591][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2022-10-15 08:09:16.591][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:09:16.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:09:16.593][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:09:16.593][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2022-10-15 08:09:16.594][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2022-10-15 08:09:16.595][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:09:16.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:09:16.596][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:09:16.597][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2022-10-15 08:09:16.597][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2022-10-15 08:09:16.602][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2022-10-15 08:09:16.603][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:09:16.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:09:16.604][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[2022-10-15 08:09:16.605][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2022-10-15 08:09:16.606][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2022-10-15 08:09:16.606][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2022-10-15 08:09:16.607][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:09:16.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:09:16.608][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:09:16.611][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2022-10-15 08:09:16.634][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-10-15 08:09:16.650][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2022-10-15 08:09:16.650][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-15 08:09:16.651][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-15 08:09:16.652][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-15 08:09:16.653][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-15 08:09:16.653][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-15 08:09:16.654][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-15 08:09:16.655][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-10-15 08:09:16.655][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-15 08:09:16.656][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-10-15 08:09:16.657][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2022-10-15 08:09:16.658][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-15 08:09:16.658][self$setPropertyValue]
biodb.DEBUG[2022-10-15 08:09:16.659][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-15 08:09:16.660][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-10-15 08:09:16.660][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-10-15 08:09:16.660][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-10-15 08:09:16.660][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2022-10-15 08:09:16.660][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2022-10-15 08:09:16.661][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-15 08:09:16.661][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-15 08:09:16.662][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-15 08:09:16.663][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-15 08:09:16.663][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-15 08:09:16.664][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-15 08:09:16.665][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-15 08:09:16.665][self$setPropertyValue]
biodb.DEBUG[2022-10-15 08:09:16.666][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-15 08:09:16.667][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-15 08:09:16.667][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-15 08:09:16.668][self$setPropertyValue]
biodb.DEBUG[2022-10-15 08:09:16.669][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2022-10-15 08:09:16.670][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-10-15 08:09:16.671][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2022-10-15 08:09:16.672][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-15 08:09:16.672][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-15 08:09:16.673][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-15 08:09:16.674][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-15 08:09:16.675][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-15 08:09:16.675][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-15 08:09:16.676][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2022-10-15 08:09:16.677][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-15 08:09:16.678][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-10-15 08:09:16.678][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2022-10-15 08:09:16.679][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-15 08:09:16.680][self$setPropertyValue]
biodb.DEBUG[2022-10-15 08:09:16.680][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-15 08:09:16.681][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-10-15 08:09:16.681][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-10-15 08:09:16.681][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-10-15 08:09:16.681][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2022-10-15 08:09:16.681][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2022-10-15 08:09:16.682][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-15 08:09:16.683][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-15 08:09:16.683][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-15 08:09:16.684][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-15 08:09:16.685][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-15 08:09:16.685][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-15 08:09:16.686][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-15 08:09:16.687][self$setPropertyValue]
biodb.DEBUG[2022-10-15 08:09:16.688][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-15 08:09:16.688][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-15 08:09:16.689][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-15 08:09:16.690][self$setPropertyValue]
biodb.DEBUG[2022-10-15 08:09:16.690][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2022-10-15 08:09:16.692][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2022-10-15 08:09:16.692][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2022-10-15 08:09:16.693][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-15 08:09:16.694][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-15 08:09:16.695][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-15 08:09:16.695][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-15 08:09:16.696][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-15 08:09:16.697][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-15 08:09:16.697][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-10-15 08:09:16.698][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-15 08:09:16.699][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2022-10-15 08:09:16.700][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2022-10-15 08:09:16.700][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-15 08:09:16.701][self$setPropertyValue]
biodb.DEBUG[2022-10-15 08:09:16.702][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-15 08:09:16.702][self$setPropertyValue]
biodb.DEBUG[2022-10-15 08:09:16.703][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-15 08:09:16.704][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-15 08:09:16.704][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-15 08:09:16.705][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-15 08:09:16.706][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-15 08:09:16.706][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-15 08:09:16.707][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-15 08:09:16.708][self$setPropertyValue]
biodb.DEBUG[2022-10-15 08:09:16.709][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-15 08:09:16.709][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-15 08:09:16.710][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-15 08:09:16.711][self$setPropertyValue]
biodb.DEBUG[2022-10-15 08:09:16.711][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2022-10-15 08:09:16.713][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2022-10-15 08:09:16.713][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2022-10-15 08:09:16.714][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-15 08:09:16.715][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-15 08:09:16.715][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-15 08:09:16.716][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-15 08:09:16.717][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-15 08:09:16.718][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-15 08:09:16.718][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2022-10-15 08:09:16.719][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-15 08:09:16.720][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2022-10-15 08:09:16.720][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2022-10-15 08:09:16.721][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-15 08:09:16.722][self$setPropertyValue]
biodb.DEBUG[2022-10-15 08:09:16.723][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-15 08:09:16.723][self$setPropertyValue]
biodb.DEBUG[2022-10-15 08:09:16.724][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-15 08:09:16.725][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-15 08:09:16.725][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-15 08:09:16.726][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-15 08:09:16.727][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-15 08:09:16.727][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-15 08:09:16.728][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-15 08:09:16.729][self$setPropertyValue]
biodb.DEBUG[2022-10-15 08:09:16.729][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-15 08:09:16.730][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-15 08:09:16.731][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-15 08:09:16.731][self$setPropertyValue]
biodb.DEBUG[2022-10-15 08:09:16.734][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-10-15 08:09:16.735][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:09:16.736][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[2022-10-15 08:09:16.736][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:09:16.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:09:16.737][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:09:16.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:09:16.739][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:09:16.739][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:09:16.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:09:16.741][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:09:16.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:09:16.742][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:09:16.743][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:09:16.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:09:16.744][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:09:16.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:09:16.745][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:09:16.746][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:09:16.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:09:16.747][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:09:16.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:09:16.748][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:09:16.749][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:09:16.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:09:16.750][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:09:16.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:09:16.755][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[2022-10-15 08:09:16.756][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:09:16.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:09:16.757][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:09:16.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:09:16.758][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:09:16.759][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:09:16.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:09:16.760][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:09:16.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:09:16.761][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:09:16.762][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:09:16.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:09:16.763][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:09:16.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:09:16.764][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[2022-10-15 08:09:16.765][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:09:16.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:09:16.766][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:09:16.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:09:16.768][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[2022-10-15 08:09:16.768][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:09:16.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:09:16.769][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:09:16.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:09:16.771][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:09:16.771][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:09:16.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:09:16.773][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:09:16.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:09:16.774][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:09:16.774][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:09:16.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:09:16.776][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:09:16.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:09:16.777][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[2022-10-15 08:09:16.778][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:09:16.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:09:16.779][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:09:16.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:09:16.780][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:09:16.781][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:09:16.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:09:16.782][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:09:16.783][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:09:16.784][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:09:16.784][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:09:16.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:09:16.785][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:09:16.786][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:09:16.787][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:09:16.787][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:09:16.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:09:16.789][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:09:16.789][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:09:16.790][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:09:16.791][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:09:16.791][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:09:16.792][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:09:16.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:09:16.793][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:09:16.794][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2022-10-15 08:09:16.797][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2022-10-15 08:09:16.798][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2022-10-15 08:09:16.799][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2022-10-15 08:09:16.800][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2022-10-15 08:09:16.801][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2022-10-15 08:09:16.802][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2022-10-15 08:09:16.803][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2022-10-15 08:09:16.804][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2022-10-15 08:09:16.805][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2022-10-15 08:09:16.806][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2022-10-15 08:09:16.807][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2022-10-15 08:09:16.808][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2022-10-15 08:09:16.809][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2022-10-15 08:09:16.810][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2022-10-15 08:09:16.811][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2022-10-15 08:09:16.812][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2022-10-15 08:09:16.813][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2022-10-15 08:09:16.814][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2022-10-15 08:09:16.815][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2022-10-15 08:09:16.816][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2022-10-15 08:09:16.817][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2022-10-15 08:09:16.818][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2022-10-15 08:09:16.819][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2022-10-15 08:09:16.820][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2022-10-15 08:09:16.821][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2022-10-15 08:09:16.822][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2022-10-15 08:09:16.823][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2022-10-15 08:09:16.824][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2022-10-15 08:09:16.825][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2022-10-15 08:09:16.826][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2022-10-15 08:09:16.827][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2022-10-15 08:09:16.828][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2022-10-15 08:09:16.829][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2022-10-15 08:09:16.830][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2022-10-15 08:09:16.830][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2022-10-15 08:09:16.831][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2022-10-15 08:09:16.832][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2022-10-15 08:09:16.833][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2022-10-15 08:09:16.834][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2022-10-15 08:09:16.835][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2022-10-15 08:09:16.836][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2022-10-15 08:09:16.837][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2022-10-15 08:09:16.838][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2022-10-15 08:09:16.839][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2022-10-15 08:09:16.840][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2022-10-15 08:09:16.841][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2022-10-15 08:09:16.842][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2022-10-15 08:09:16.843][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2022-10-15 08:09:16.844][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2022-10-15 08:09:16.845][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2022-10-15 08:09:16.846][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2022-10-15 08:09:16.847][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2022-10-15 08:09:16.848][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2022-10-15 08:09:16.849][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2022-10-15 08:09:16.850][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2022-10-15 08:09:16.851][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2022-10-15 08:09:16.852][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2022-10-15 08:09:16.853][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2022-10-15 08:09:16.854][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2022-10-15 08:09:16.855][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2022-10-15 08:09:16.856][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2022-10-15 08:09:16.857][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2022-10-15 08:09:16.858][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2022-10-15 08:09:16.859][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2022-10-15 08:09:16.860][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2022-10-15 08:09:16.861][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2022-10-15 08:09:16.862][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2022-10-15 08:09:16.862][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2022-10-15 08:09:16.863][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2022-10-15 08:09:16.864][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2022-10-15 08:09:16.869][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2022-10-15 08:09:16.870][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2022-10-15 08:09:16.871][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2022-10-15 08:09:16.872][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2022-10-15 08:09:16.873][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2022-10-15 08:09:16.874][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2022-10-15 08:09:16.875][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2022-10-15 08:09:16.876][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2022-10-15 08:09:16.877][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2022-10-15 08:09:16.878][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2022-10-15 08:09:16.879][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2022-10-15 08:09:16.879][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2022-10-15 08:09:16.883][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2022-10-15 08:09:16.885][initialize] This is biodb version 1.4.2.
biodb.DEBUG[2022-10-15 08:09:16.887][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-10-15 08:09:16.888][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:09:16.888][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:09:16.889][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:09:16.890][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:09:16.893][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:09:16.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:09:16.894][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:09:16.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:09:16.895][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:09:16.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:09:16.896][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:09:16.897][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:09:16.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:09:16.898][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:09:16.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:09:16.900][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:09:16.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:09:16.901][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:09:16.902][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:09:16.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:09:16.903][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:09:16.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:09:16.904][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:09:16.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:09:16.905][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:09:16.906][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:09:16.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:09:16.907][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:09:16.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:09:16.909][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:09:16.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:09:16.910][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:09:16.910][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:09:16.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:09:16.912][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:09:16.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:09:16.913][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:09:16.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:09:16.914][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:09:16.915][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:09:16.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:09:16.916][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:09:16.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:09:16.918][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:09:16.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:09:16.919][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:09:16.920][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:09:16.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:09:16.921][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:09:16.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:09:16.922][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:09:16.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:09:16.923][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:09:16.924][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:09:16.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:09:16.925][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:09:16.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:09:16.927][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:09:16.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:09:16.928][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:09:16.928][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:09:16.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:09:16.930][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:09:16.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:09:16.931][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:09:16.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:09:16.932][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:09:16.933][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:09:16.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:09:16.934][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:09:16.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:09:16.935][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:09:16.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:09:16.937][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:09:16.937][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:09:16.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:09:16.939][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:09:16.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:09:16.940][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:09:16.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:09:16.941][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:09:16.942][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:09:16.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:09:16.943][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:09:16.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:09:16.944][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:09:16.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:09:16.946][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:09:16.946][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:09:16.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:09:16.947][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:09:16.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:09:16.949][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:09:16.949][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:09:16.950][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:09:16.951][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:09:16.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:09:16.952][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:09:16.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:09:16.953][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:09:16.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:09:16.954][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:09:16.955][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:09:16.956][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:09:16.956][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:09:16.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:09:16.958][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:09:16.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:09:16.959][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:09:16.960][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:09:16.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:09:16.961][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:09:16.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:09:16.962][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:09:16.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:09:16.963][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:09:16.964][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:09:16.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:09:16.965][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:09:16.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:09:16.966][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:09:16.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:09:16.968][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:09:16.969][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.15-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2022-10-15 08:09:16.997][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2022-10-15 08:09:16.998][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-10-15 08:09:16.999][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2022-10-15 08:09:17.000][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-15 08:09:17.001][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-15 08:09:17.001][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2022-10-15 08:09:17.002][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2022-10-15 08:09:17.003][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2022-10-15 08:09:17.003][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-15 08:09:17.004][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2022-10-15 08:09:17.005][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-15 08:09:17.005][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-10-15 08:09:17.006][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2022-10-15 08:09:17.007][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-15 08:09:17.008][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2022-10-15 08:09:17.008][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2022-10-15 08:09:17.008][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2022-10-15 08:09:17.008][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2022-10-15 08:09:17.008][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2022-10-15 08:09:17.008][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2022-10-15 08:09:17.008][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2022-10-15 08:09:17.008][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2022-10-15 08:09:17.009][self$setPropertyValue]
biodb.DEBUG[2022-10-15 08:09:17.010][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2022-10-15 08:09:17.010][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-15 08:09:17.011][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-15 08:09:17.012][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-15 08:09:17.012][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-15 08:09:17.013][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-15 08:09:17.014][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-15 08:09:17.014][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2022-10-15 08:09:17.014][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2022-10-15 08:09:17.014][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2022-10-15 08:09:17.014][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2022-10-15 08:09:17.015][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-15 08:09:17.016][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-15 08:09:17.017][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2022-10-15 08:09:17.017][self$setPropertyValue]
biodb.DEBUG[2022-10-15 08:09:17.021][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2022-10-15 08:09:17.038][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2022-10-15 08:09:17.039][super$initialize] Register connector nci.cactus with the request scheduler
biodb.DEBUG[2022-10-15 08:09:17.042][private$bdb$getRequestScheduler()$re ...] Register connector nci.cactus.
biodb.DEBUG[2022-10-15 08:09:17.044][private$addConnectorRules] Create new rule for URL "cactus.nci.nih.gov" of connector "nci.cactus".
biodb.DEBUG[2022-10-15 08:09:17.047][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2022-10-15 08:09:17.048][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2022-10-15 08:09:17.049][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2022-10-15 08:09:17.050][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2022-10-15 08:09:17.051][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2022-10-15 08:09:17.052][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2022-10-15 08:09:17.063][biodb::testThat]
biodb.INFO [2022-10-15 08:09:17.064][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2022-10-15 08:09:17.065][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-15 08:09:17.065][biodb::testThat]
biodb.TRACE[2022-10-15 08:09:17.068][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.15-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-749674-content.sdf".
biodb.DEBUG[2022-10-15 08:09:17.071][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2022-10-15 08:09:17.073][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2022-10-15 08:09:17.079][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-15 08:09:17.080][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:09:17.080][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:09:17.089][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:09:17.090][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:09:17.090][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:09:17.091][FUN] Functions in observer BiodbConfig: [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[2022-10-15 08:09:17.103][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:09:17.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:09:17.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.106][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:09:17.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:09:17.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.119][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-15 08:09:17.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-15 08:09:17.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.144][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-15 08:09:17.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-15 08:09:17.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.149][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-15 08:09:17.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-15 08:09:17.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.152][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-15 08:09:17.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-15 08:09:17.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.158][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-10-15 08:09:17.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-15 08:09:17.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.161][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-10-15 08:09:17.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-15 08:09:17.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.166][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-15 08:09:17.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-15 08:09:17.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.169][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-15 08:09:17.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-15 08:09:17.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.174][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2022-10-15 08:09:17.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2022-10-15 08:09:17.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.177][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2022-10-15 08:09:17.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2022-10-15 08:09:17.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.180][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:09:17.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:09:17.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.183][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2022-10-15 08:09:17.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2022-10-15 08:09:17.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.186][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:09:17.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:09:17.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.189][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:09:17.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:09:17.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.191][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:09:17.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:09:17.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.227][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:09:17.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:09:17.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.231][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:09:17.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:09:17.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.234][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:09:17.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:09:17.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-15 08:09:17.238][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 749674.
biodb.TRACE[2022-10-15 08:09:17.244][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-10-15 08:09:17.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-10-15 08:09:17.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.247][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-10-15 08:09:17.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-10-15 08:09:17.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.250][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2022-10-15 08:09:17.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2022-10-15 08:09:17.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.253][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2022-10-15 08:09:17.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2022-10-15 08:09:17.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.269][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:09:17.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:09:17.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.282][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2022-10-15 08:09:17.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2022-10-15 08:09:17.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.288][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:09:17.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:09:17.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.291][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:09:17.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:09:17.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.294][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:09:17.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:09:17.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.298][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:09:17.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:09:17.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.301][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:09:17.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:09:17.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.304][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:09:17.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:09:17.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.308][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2022-10-15 08:09:17.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2022-10-15 08:09:17.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.311][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2022-10-15 08:09:17.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2022-10-15 08:09:17.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.320][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2022-10-15 08:09:17.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2022-10-15 08:09:17.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.328][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:09:17.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:09:17.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.331][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:09:17.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:09:17.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.334][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:09:17.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:09:17.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.337][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:09:17.337][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:09:17.338][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.339][ef$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.340][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:09:17.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:09:17.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.347][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-15 08:09:17.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-15 08:09:17.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.350][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-15 08:09:17.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-15 08:09:17.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.353][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-15 08:09:17.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-15 08:09:17.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.356][ef$get] Asked field names are: formula.
biodb.TRACE[2022-10-15 08:09:17.357][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-15 08:09:17.357][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.358][ef$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.359][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-15 08:09:17.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-15 08:09:17.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.366][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-15 08:09:17.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-15 08:09:17.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.369][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-15 08:09:17.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-15 08:09:17.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.372][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-15 08:09:17.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-15 08:09:17.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.375][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-15 08:09:17.376][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-15 08:09:17.376][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.377][ef$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.378][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-15 08:09:17.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-15 08:09:17.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.385][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-10-15 08:09:17.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-15 08:09:17.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.388][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-10-15 08:09:17.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-15 08:09:17.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.391][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-10-15 08:09:17.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-15 08:09:17.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.394][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-10-15 08:09:17.395][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-15 08:09:17.395][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.396][ef$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.397][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-10-15 08:09:17.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-15 08:09:17.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.404][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-15 08:09:17.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-15 08:09:17.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.410][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-15 08:09:17.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-15 08:09:17.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.413][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-15 08:09:17.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-15 08:09:17.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.416][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-15 08:09:17.416][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-15 08:09:17.417][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.418][ef$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.418][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-15 08:09:17.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-15 08:09:17.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.425][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:09:17.426][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:09:17.427][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.428][ef$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.431][ef$get] Asked field names are: formula.
biodb.TRACE[2022-10-15 08:09:17.432][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-15 08:09:17.432][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.433][ef$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.436][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-10-15 08:09:17.437][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-15 08:09:17.438][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.439][ef$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.442][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-15 08:09:17.443][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-15 08:09:17.443][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.444][ef$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.447][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-15 08:09:17.448][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-15 08:09:17.449][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.449][ef$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.461][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.15-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-750690-content.sdf".
biodb.DEBUG[2022-10-15 08:09:17.489][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2022-10-15 08:09:17.490][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2022-10-15 08:09:17.491][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-15 08:09:17.492][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:09:17.492][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:09:17.496][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:09:17.496][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:09:17.497][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:09:17.498][FUN] Functions in observer BiodbConfig: [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[2022-10-15 08:09:17.503][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:09:17.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:09:17.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.506][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:09:17.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:09:17.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.522][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2022-10-15 08:09:17.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2022-10-15 08:09:17.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.525][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2022-10-15 08:09:17.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2022-10-15 08:09:17.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.530][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-15 08:09:17.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-15 08:09:17.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.533][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-15 08:09:17.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-15 08:09:17.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.538][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-15 08:09:17.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-15 08:09:17.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.541][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-15 08:09:17.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-15 08:09:17.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.545][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-15 08:09:17.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-15 08:09:17.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.548][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-15 08:09:17.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-15 08:09:17.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.553][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-15 08:09:17.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-15 08:09:17.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.556][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-15 08:09:17.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-15 08:09:17.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.559][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-15 08:09:17.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-15 08:09:17.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.562][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-15 08:09:17.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-15 08:09:17.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.568][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-15 08:09:17.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-15 08:09:17.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.573][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-10-15 08:09:17.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-15 08:09:17.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.575][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-10-15 08:09:17.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-15 08:09:17.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.580][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-15 08:09:17.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-15 08:09:17.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.583][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-15 08:09:17.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-15 08:09:17.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.588][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2022-10-15 08:09:17.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2022-10-15 08:09:17.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.591][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2022-10-15 08:09:17.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2022-10-15 08:09:17.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.594][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:09:17.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:09:17.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.597][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2022-10-15 08:09:17.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2022-10-15 08:09:17.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.600][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:09:17.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:09:17.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.602][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:09:17.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:09:17.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.605][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:09:17.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:09:17.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.610][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:09:17.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:09:17.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.613][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:09:17.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:09:17.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.616][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:09:17.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:09:17.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-15 08:09:17.619][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 750690.
biodb.TRACE[2022-10-15 08:09:17.634][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-10-15 08:09:17.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-10-15 08:09:17.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.636][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-10-15 08:09:17.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-10-15 08:09:17.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.639][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2022-10-15 08:09:17.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2022-10-15 08:09:17.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.642][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2022-10-15 08:09:17.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2022-10-15 08:09:17.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.646][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:09:17.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:09:17.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.655][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2022-10-15 08:09:17.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2022-10-15 08:09:17.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.660][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:09:17.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:09:17.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.663][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:09:17.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:09:17.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.666][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:09:17.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:09:17.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.670][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:09:17.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:09:17.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.673][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:09:17.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:09:17.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.676][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:09:17.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:09:17.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.679][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2022-10-15 08:09:17.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2022-10-15 08:09:17.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.682][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2022-10-15 08:09:17.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2022-10-15 08:09:17.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.685][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2022-10-15 08:09:17.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2022-10-15 08:09:17.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.698][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:09:17.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:09:17.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.701][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:09:17.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:09:17.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.704][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:09:17.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:09:17.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.707][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:09:17.708][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:09:17.709][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.709][ef$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.710][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:09:17.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:09:17.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.717][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2022-10-15 08:09:17.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2022-10-15 08:09:17.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.720][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2022-10-15 08:09:17.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2022-10-15 08:09:17.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.723][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2022-10-15 08:09:17.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2022-10-15 08:09:17.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.726][ef$get] Asked field names are: cas.id.
biodb.TRACE[2022-10-15 08:09:17.727][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2022-10-15 08:09:17.727][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.728][ef$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.729][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2022-10-15 08:09:17.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2022-10-15 08:09:17.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.740][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-15 08:09:17.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-15 08:09:17.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.743][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-15 08:09:17.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-15 08:09:17.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.746][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-15 08:09:17.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-15 08:09:17.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.748][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-15 08:09:17.749][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-15 08:09:17.750][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.750][ef$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.751][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-15 08:09:17.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-15 08:09:17.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.759][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-15 08:09:17.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-15 08:09:17.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.762][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-15 08:09:17.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-15 08:09:17.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.764][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-15 08:09:17.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-15 08:09:17.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.767][ef$get] Asked field names are: formula.
biodb.TRACE[2022-10-15 08:09:17.768][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-15 08:09:17.769][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.769][ef$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.770][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-15 08:09:17.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-15 08:09:17.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.777][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-15 08:09:17.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-15 08:09:17.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.780][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-15 08:09:17.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-15 08:09:17.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.783][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-15 08:09:17.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-15 08:09:17.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.786][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-15 08:09:17.786][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-15 08:09:17.787][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.788][ef$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.789][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-15 08:09:17.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-15 08:09:17.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.796][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-10-15 08:09:17.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-15 08:09:17.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.798][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-10-15 08:09:17.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-15 08:09:17.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.801][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-10-15 08:09:17.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-15 08:09:17.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.804][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-10-15 08:09:17.805][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-15 08:09:17.806][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.806][ef$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.807][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-10-15 08:09:17.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-15 08:09:17.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.814][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-15 08:09:17.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-15 08:09:17.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.817][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-15 08:09:17.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-15 08:09:17.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.820][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-15 08:09:17.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-15 08:09:17.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.826][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-15 08:09:17.826][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-15 08:09:17.827][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.828][ef$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.828][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-15 08:09:17.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-15 08:09:17.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.835][ef$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:09:17.836][ef$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:09:17.837][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.838][ef$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.841][ef$get] Asked field names are: cas.id.
biodb.TRACE[2022-10-15 08:09:17.842][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2022-10-15 08:09:17.842][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.843][ef$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.846][ef$get] Asked field names are: formula.
biodb.TRACE[2022-10-15 08:09:17.847][ef$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-15 08:09:17.848][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.849][ef$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.852][ef$get] Asked field names are: inchi.
biodb.TRACE[2022-10-15 08:09:17.853][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-15 08:09:17.853][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.854][ef$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.857][ef$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-15 08:09:17.858][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-15 08:09:17.859][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.860][ef$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.863][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-15 08:09:17.864][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-15 08:09:17.864][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.865][ef$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:09:17.868][ef$get] Asked field names are: name.
biodb.TRACE[2022-10-15 08:09:17.869][ef$get] Realnames of fields are: name.
biodb.TRACE[2022-10-15 08:09:17.870][ef$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:09:17.871][ef$get] fields variable is a list.
biodb.INFO [2022-10-15 08:09:17.875][biodb::testThat]
biodb.INFO [2022-10-15 08:09:17.875][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2022-10-15 08:09:17.876][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-15 08:09:17.877][biodb::testThat]
biodb.DEBUG[2022-10-15 08:09:17.878][private$loadEntries] Creating entries from ids [2]: "749674, 750690".
biodb.DEBUG[2022-10-15 08:09:17.884][conn$getEntryContent] Get NCI CACTUS entry content(s) for 2 id(s)...
biodb.INFO [2022-10-15 08:09:17.886][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427" for "nci.cactus-8efc65070d01b214e760b1d4932ee427".
biodb.DEBUG[2022-10-15 08:09:17.887][self$isDownloaded] Database nci.cactus has not yet been downloaded.
biodb.INFO [2022-10-15 08:09:17.888][self$download] Downloading whole database of nci.cactus.
biodb.INFO [2022-10-15 08:09:17.889][private$doDownload] Downloading NCI CACTUS database at "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz" ...
biodb.DEBUG[2022-10-15 08:09:17.890][sched$downloadFile] Downloading file "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
trying URL 'https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz'
Content type 'application/x-gzip' length 206737123 bytes (197.2 MB)
==================================================
downloaded 197.2 MB

biodb.TRACE[2022-10-15 08:09:50.033][cch$addFilesToCache] Moving files to cache [1]: "/home/biocbuild/.cache/R/biodb/tmp/nci.cactus2453e55ae3d5c1gz".
biodb.TRACE[2022-10-15 08:09:50.036][private$doAddFilesToCache] Destination files are [1]: "/home/biocbuild/.cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/download.gz".
biodb.DEBUG[2022-10-15 08:09:50.036][cch$addFilesToCache] Done adding files.
biodb.DEBUG[2022-10-15 08:09:50.038][self$getDownloadPath] Download path of nci.cactus is "/home/biocbuild/.cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/download.gz".
biodb.DEBUG[2022-10-15 08:09:50.038][self$download] Downloading of nci.cactus completed.
biodb.TRACE[2022-10-15 08:09:50.040][self$addFilesToCache] Moving files to cache [1]: "/home/biocbuild/.cache/R/biodb/tmp/marker2453e545c931c7marker".
biodb.TRACE[2022-10-15 08:09:50.041][private$doAddFilesToCache] Destination files are [1]: "/home/biocbuild/.cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/downloaded.marker".
biodb.DEBUG[2022-10-15 08:09:50.041][self$addFilesToCache] Done adding files.
biodb.DEBUG[2022-10-15 08:09:50.042][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.INFO [2022-10-15 08:09:50.044][self$download] Extract whole database of nci.cactus.
biodb.INFO [2022-10-15 08:09:50.044][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database....
biodb.DEBUG[2022-10-15 08:09:50.045][self$getDownloadPath] Download path of nci.cactus is "/home/biocbuild/.cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/download.gz".
biodb.DEBUG[2022-10-15 08:10:46.572][private$doExtractDownload] Delete existing entry files in cache system.
biodb.DEBUG[2022-10-15 08:10:46.573][private$doExtractDownload] Extract single entries from downloaded file "/home/biocbuild/.cache/R/biodb/tmp/cactus_rdfs", into "/home/biocbuild/.cache/R/biodb/tmp".
biodb.TRACE[2022-10-15 08:18:50.206][self$addFilesToCache] Moving files to cache [265242]: "/home/biocbuild/.cache/R/biodb/tmp/entry_1.txt, /home/biocbuild/.cache/R/biodb/tmp/entry_2.txt, /home/biocbuild/.cache/R/biodb/tmp/entry_3.txt, /home/biocbuild/.cache/R/biodb/tmp/entry_4.txt, /home/biocbuild/.cache/R/biodb/tmp/entry_5.txt, /home/biocbuild/.cache/R/biodb/tmp/entry_6.txt, /home/biocbuild/.cache/R/biodb/tmp/entry_7.txt, /home/biocbuild/.cache/R/biodb/tmp/entry_8.txt, /home/biocbuild/.cache/R/biodb/tmp/entry_9.txt, /home/biocbuild/.cache/R/biodb/tmp/entry_10.txt, ...".
biodb.TRACE[2022-10-15 08:18:50.488][private$doAddFilesToCache] Destination files are [265242]: "/home/biocbuild/.cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/1.sdf, /home/biocbuild/.cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/2.sdf, /home/biocbuild/.cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/3.sdf, /home/biocbuild/.cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/4.sdf, /home/biocbuild/.cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/5.sdf, /home/biocbuild/.cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/6.sdf, /home/biocbuild/.cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/7.sdf, /home/biocbuild/.cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/8.sdf, /home/biocbuild/.cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/9.sdf, /home/biocbuild/.cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/10.sdf, ...".
biodb.DEBUG[2022-10-15 08:18:58.271][self$addFilesToCache] Done adding files.
biodb.DEBUG[2022-10-15 08:18:58.272][private$doExtractDownload] Delete extracted database.
biodb.TRACE[2022-10-15 08:18:58.281][self$addFilesToCache] Moving files to cache [1]: "/home/biocbuild/.cache/R/biodb/tmp/marker2453e52086c380marker".
biodb.TRACE[2022-10-15 08:18:58.282][private$doAddFilesToCache] Destination files are [1]: "/home/biocbuild/.cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/extracted.marker".
biodb.DEBUG[2022-10-15 08:18:58.283][self$addFilesToCache] Done adding files.
biodb.TRACE[2022-10-15 08:18:58.285][cch$loadFileContent] Trying to load 2 files from cache: [2]: "749674, 750690".
biodb.TRACE[2022-10-15 08:18:58.285][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2022-10-15 08:18:58.287][loadFileContents] Loaded 2 files from cache: [2]: "/home/biocbuild/.cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/749674.sdf, /home/biocbuild/.cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/750690.sdf".
biodb.DEBUG[2022-10-15 08:18:58.288][conn$getEntryContent] 2 NCI CACTUS entry content(s) loaded from cache.
biodb.DEBUG[2022-10-15 08:18:58.304][self$createEntryFromContent] Creating NCI CACTUS entries from 2 content(s).
biodb.DEBUG[2022-10-15 08:18:58.305][self$createEntryFromContent] Parsing 2 NCI CACTUS entries.
biodb.DEBUG[2022-10-15 08:18:58.306][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-15 08:18:58.307][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:18:58.307][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:18:58.311][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:18:58.312][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:18:58.313][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:18:58.314][FUN] Functions in observer BiodbConfig: [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[2022-10-15 08:18:58.319][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:18:58.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:18:58.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:18:58.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:18:58.322][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:18:58.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:18:58.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:18:58.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:18:58.328][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-15 08:18:58.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-15 08:18:58.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:18:58.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:18:58.331][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-15 08:18:58.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-15 08:18:58.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:18:58.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:18:58.337][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-15 08:18:58.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-15 08:18:58.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:18:58.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:18:58.340][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-15 08:18:58.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-15 08:18:58.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:18:58.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:18:58.345][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-10-15 08:18:58.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-15 08:18:58.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:18:58.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:18:58.349][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-10-15 08:18:58.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-15 08:18:58.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:18:58.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:18:58.354][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-15 08:18:58.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-15 08:18:58.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:18:58.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:18:58.357][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-15 08:18:58.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-15 08:18:58.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:18:58.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:18:58.362][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2022-10-15 08:18:58.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2022-10-15 08:18:58.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:18:58.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:18:58.365][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2022-10-15 08:18:58.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2022-10-15 08:18:58.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:18:58.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:18:58.368][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:18:58.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:18:58.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:18:58.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:18:58.371][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2022-10-15 08:18:58.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2022-10-15 08:18:58.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:18:58.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:18:58.374][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:18:58.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:18:58.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:18:58.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:18:58.377][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:18:58.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:18:58.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:18:58.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:18:58.380][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:18:58.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:18:58.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:18:58.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-15 08:18:58.386][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2022-10-15 08:18:58.386][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:18:58.387][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:18:58.391][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:18:58.392][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:18:58.393][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:18:58.393][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2022-10-15 08:18:58.399][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:18:58.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:18:58.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:18:58.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:18:58.402][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:18:58.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:18:58.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:18:58.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:18:58.408][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2022-10-15 08:18:58.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2022-10-15 08:18:58.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:18:58.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:18:58.411][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2022-10-15 08:18:58.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2022-10-15 08:18:58.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:18:58.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:18:58.417][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-15 08:18:58.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-15 08:18:58.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:18:58.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:18:58.420][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2022-10-15 08:18:58.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2022-10-15 08:18:58.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:18:58.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:18:58.425][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-15 08:18:58.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-15 08:18:58.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:18:58.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:18:58.428][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2022-10-15 08:18:58.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2022-10-15 08:18:58.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:18:58.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:18:58.433][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-15 08:18:58.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-15 08:18:58.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:18:58.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:18:58.436][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-15 08:18:58.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-15 08:18:58.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:18:58.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:18:58.441][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-15 08:18:58.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-15 08:18:58.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:18:58.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:18:58.444][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-15 08:18:58.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-15 08:18:58.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:18:58.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:18:58.447][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-15 08:18:58.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-15 08:18:58.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:18:58.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:18:58.451][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-15 08:18:58.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-15 08:18:58.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:18:58.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:18:58.454][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2022-10-15 08:18:58.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2022-10-15 08:18:58.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:18:58.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:18:58.459][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-10-15 08:18:58.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-15 08:18:58.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:18:58.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:18:58.462][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2022-10-15 08:18:58.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2022-10-15 08:18:58.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:18:58.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:18:58.468][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-15 08:18:58.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-15 08:18:58.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:18:58.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:18:58.471][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2022-10-15 08:18:58.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2022-10-15 08:18:58.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:18:58.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:18:58.476][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2022-10-15 08:18:58.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2022-10-15 08:18:58.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:18:58.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:18:58.479][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2022-10-15 08:18:58.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2022-10-15 08:18:58.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:18:58.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:18:58.482][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:18:58.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:18:58.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:18:58.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:18:58.485][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2022-10-15 08:18:58.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2022-10-15 08:18:58.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:18:58.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:18:58.488][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:18:58.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:18:58.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:18:58.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:18:58.491][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:18:58.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:18:58.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:18:58.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:18:58.494][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:18:58.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:18:58.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:18:58.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:18:58.499][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:18:58.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:18:58.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:18:58.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:18:58.502][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:18:58.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:18:58.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:18:58.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:18:58.505][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:18:58.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:18:58.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:18:58.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:18:58.508][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:18:58.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:18:58.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:18:58.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:18:58.512][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:18:58.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:18:58.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:18:58.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:18:58.514][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2022-10-15 08:18:58.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2022-10-15 08:18:58.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:18:58.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2022-10-15 08:18:58.517][self$createEntryFromContent] Accession numbers: 749674, 750690.
biodb.TRACE[2022-10-15 08:18:58.518][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2022-10-15 08:18:58.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2022-10-15 08:18:58.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:18:58.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:18:58.521][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2022-10-15 08:18:58.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2022-10-15 08:18:58.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:18:58.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:18:58.524][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2022-10-15 08:18:58.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2022-10-15 08:18:58.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:18:58.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:18:58.531][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2022-10-15 08:18:58.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2022-10-15 08:18:58.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:18:58.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:18:58.534][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2022-10-15 08:18:58.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2022-10-15 08:18:58.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:18:58.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:18:58.537][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2022-10-15 08:18:58.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2022-10-15 08:18:58.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:18:58.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2022-10-15 08:18:58.544][biodb::testThat]
biodb.INFO [2022-10-15 08:18:58.545][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2022-10-15 08:18:58.545][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-15 08:18:58.546][biodb::testThat]
biodb.INFO [2022-10-15 08:18:58.549][biodb::testThat]
biodb.INFO [2022-10-15 08:18:58.549][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2022-10-15 08:18:58.550][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-15 08:18:58.551][biodb::testThat]
biodb.WARN [2022-10-15 08:18:58.575][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2022-10-15 08:18:58.595][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2022-10-15 08:18:58.602][biodb::testThat]
biodb.INFO [2022-10-15 08:18:58.603][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2022-10-15 08:18:58.604][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-15 08:18:58.604][biodb::testThat]
biodb.TRACE[2022-10-15 08:18:58.625][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-10-15 08:18:58.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-10-15 08:18:58.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:18:58.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:18:58.628][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-10-15 08:18:58.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-10-15 08:18:58.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:18:58.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:18:58.631][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2022-10-15 08:18:58.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2022-10-15 08:18:58.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:18:58.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:18:58.635][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2022-10-15 08:18:58.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2022-10-15 08:18:58.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:18:58.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:18:58.662][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-10-15 08:18:58.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-10-15 08:18:58.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:18:58.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:18:58.665][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2022-10-15 08:18:58.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2022-10-15 08:18:58.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:18:58.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:18:58.669][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2022-10-15 08:18:58.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2022-10-15 08:18:58.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:18:58.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2022-10-15 08:18:58.672][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2022-10-15 08:18:58.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2022-10-15 08:18:58.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2022-10-15 08:18:58.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2022-10-15 08:18:58.676][biodb::testThat]
biodb.INFO [2022-10-15 08:18:58.677][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2022-10-15 08:18:58.678][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-15 08:18:58.679][biodb::testThat]
biodb.INFO [2022-10-15 08:18:58.682][biodb::testThat]
biodb.INFO [2022-10-15 08:18:58.683][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2022-10-15 08:18:58.683][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-15 08:18:58.684][biodb::testThat]
biodb.INFO [2022-10-15 08:18:58.687][biodb::testThat]
biodb.INFO [2022-10-15 08:18:58.688][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2022-10-15 08:18:58.689][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-15 08:18:58.689][biodb::testThat]
biodb.INFO [2022-10-15 08:18:58.692][biodb::testThat]
biodb.INFO [2022-10-15 08:18:58.693][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2022-10-15 08:18:58.693][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2022-10-15 08:18:58.694][biodb::testThat]
biodb.INFO [2022-10-15 08:18:58.705][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2022-10-15 08:18:58.705][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector nci.cactus from the request scheduler
biodb.INFO [2022-10-15 08:18:58.706][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2022-10-15 08:18:58.707][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2022-10-15 08:18:58.708][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:18:58.708][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:18:58.709][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:18:58.710][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:18:58.710][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:18:58.711][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2022-10-15 08:18:58.718][biodb::testContext]
biodb.INFO [2022-10-15 08:18:58.719][biodb::testContext] ********************************************************************************
biodb.INFO [2022-10-15 08:18:58.719][biodb::testContext] Test context - Example long tests
biodb.INFO [2022-10-15 08:18:58.720][biodb::testContext] ********************************************************************************
biodb.INFO [2022-10-15 08:18:58.721][biodb::testContext]
biodb.INFO [2022-10-15 08:18:58.724][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.4.2.
biodb.DEBUG[2022-10-15 08:18:58.725][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.15-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2022-10-15 08:18:58.728][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-10-15 08:18:58.729][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2022-10-15 08:18:58.730][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2022-10-15 08:18:58.731][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:18:58.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:18:58.732][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[2022-10-15 08:18:58.733][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2022-10-15 08:18:58.734][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2022-10-15 08:18:58.734][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:18:58.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:18:58.736][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:18:58.737][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2022-10-15 08:18:58.737][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2022-10-15 08:18:58.738][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:18:58.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:18:58.740][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:18:58.741][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2022-10-15 08:18:58.741][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2022-10-15 08:18:58.742][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2022-10-15 08:18:58.743][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:18:58.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:18:58.744][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:18:58.745][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2022-10-15 08:18:58.746][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2022-10-15 08:18:58.747][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2022-10-15 08:18:58.748][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:18:58.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:18:58.749][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:18:58.750][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2022-10-15 08:18:58.751][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2022-10-15 08:18:58.752][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:18:58.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:18:58.753][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:18:58.754][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2022-10-15 08:18:58.755][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2022-10-15 08:18:58.756][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2022-10-15 08:18:58.756][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:18:58.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:18:58.758][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:18:58.759][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2022-10-15 08:18:58.760][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2022-10-15 08:18:58.760][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:18:58.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:18:58.762][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:18:58.763][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2022-10-15 08:18:58.763][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2022-10-15 08:18:58.764][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2022-10-15 08:18:58.765][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:18:58.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:18:58.766][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:18:58.767][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2022-10-15 08:18:58.768][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2022-10-15 08:18:58.769][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2022-10-15 08:18:58.770][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2022-10-15 08:18:58.771][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2022-10-15 08:18:58.772][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2022-10-15 08:18:58.772][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:18:58.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:18:58.774][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:18:58.774][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2022-10-15 08:18:58.775][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2022-10-15 08:18:58.776][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:18:58.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:18:58.777][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[2022-10-15 08:18:58.778][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2022-10-15 08:18:58.779][self$set] Set key entries.sep to "|".
biodb.DEBUG[2022-10-15 08:18:58.780][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:18:58.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:18:58.781][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:18:58.782][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2022-10-15 08:18:58.783][self$set] Set key offline to FALSE.
biodb.DEBUG[2022-10-15 08:18:58.784][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:18:58.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:18:58.785][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:18:58.786][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2022-10-15 08:18:58.787][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2022-10-15 08:18:58.788][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:18:58.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:18:58.789][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:18:58.790][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2022-10-15 08:18:58.791][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2022-10-15 08:18:58.791][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:18:58.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:18:58.793][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:18:58.794][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2022-10-15 08:18:58.794][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2022-10-15 08:18:58.799][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2022-10-15 08:18:58.800][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:18:58.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:18:58.801][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:18:58.802][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2022-10-15 08:18:58.803][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2022-10-15 08:18:58.804][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2022-10-15 08:18:58.805][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:18:58.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:18:58.806][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:18:58.807][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2022-10-15 08:18:58.809][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-10-15 08:18:58.810][self$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[2022-10-15 08:18:58.810][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-15 08:18:58.811][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-15 08:18:58.812][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-15 08:18:58.813][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-15 08:18:58.814][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-15 08:18:58.815][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-15 08:18:58.816][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-10-15 08:18:58.817][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-15 08:18:58.817][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-10-15 08:18:58.818][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2022-10-15 08:18:58.819][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-15 08:18:58.820][self$setPropertyValue]
biodb.DEBUG[2022-10-15 08:18:58.821][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-15 08:18:58.822][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-10-15 08:18:58.822][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-10-15 08:18:58.822][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-10-15 08:18:58.822][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2022-10-15 08:18:58.822][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2022-10-15 08:18:58.822][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-15 08:18:58.823][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-15 08:18:58.824][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-15 08:18:58.825][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-15 08:18:58.826][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-15 08:18:58.826][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-15 08:18:58.827][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-15 08:18:58.828][self$setPropertyValue]
biodb.DEBUG[2022-10-15 08:18:58.829][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-15 08:18:58.829][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-15 08:18:58.830][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-15 08:18:58.831][self$setPropertyValue]
biodb.DEBUG[2022-10-15 08:18:58.832][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2022-10-15 08:18:58.834][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-10-15 08:18:58.834][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2022-10-15 08:18:58.835][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-15 08:18:58.836][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-15 08:18:58.837][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-15 08:18:58.838][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-15 08:18:58.839][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-15 08:18:58.839][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-15 08:18:58.840][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2022-10-15 08:18:58.841][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-15 08:18:58.842][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-10-15 08:18:58.843][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2022-10-15 08:18:58.844][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-15 08:18:58.844][self$setPropertyValue]
biodb.DEBUG[2022-10-15 08:18:58.845][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-15 08:18:58.846][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2022-10-15 08:18:58.846][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2022-10-15 08:18:58.846][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2022-10-15 08:18:58.846][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2022-10-15 08:18:58.846][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2022-10-15 08:18:58.847][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-15 08:18:58.848][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-15 08:18:58.848][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-15 08:18:58.849][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-15 08:18:58.850][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-15 08:18:58.851][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-15 08:18:58.851][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-15 08:18:58.852][self$setPropertyValue]
biodb.DEBUG[2022-10-15 08:18:58.853][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-15 08:18:58.854][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-15 08:18:58.855][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-15 08:18:58.855][self$setPropertyValue]
biodb.DEBUG[2022-10-15 08:18:58.856][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2022-10-15 08:18:58.858][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2022-10-15 08:18:58.859][self$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[2022-10-15 08:18:58.859][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-15 08:18:58.860][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-15 08:18:58.861][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-15 08:18:58.862][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-15 08:18:58.863][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-15 08:18:58.863][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-15 08:18:58.864][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2022-10-15 08:18:58.865][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-15 08:18:58.866][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2022-10-15 08:18:58.867][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2022-10-15 08:18:58.868][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-15 08:18:58.868][self$setPropertyValue]
biodb.DEBUG[2022-10-15 08:18:58.869][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-15 08:18:58.870][self$setPropertyValue]
biodb.DEBUG[2022-10-15 08:18:58.871][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-15 08:18:58.872][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-15 08:18:58.873][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-15 08:18:58.873][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-15 08:18:58.874][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-15 08:18:58.875][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-15 08:18:58.876][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-15 08:18:58.877][self$setPropertyValue]
biodb.DEBUG[2022-10-15 08:18:58.877][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-15 08:18:58.878][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-15 08:18:58.879][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-15 08:18:58.880][self$setPropertyValue]
biodb.DEBUG[2022-10-15 08:18:58.881][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2022-10-15 08:18:58.882][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2022-10-15 08:18:58.883][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2022-10-15 08:18:58.884][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-15 08:18:58.885][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-15 08:18:58.885][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2022-10-15 08:18:58.886][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2022-10-15 08:18:58.887][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2022-10-15 08:18:58.888][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-15 08:18:58.889][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2022-10-15 08:18:58.890][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-15 08:18:58.891][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2022-10-15 08:18:58.892][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2022-10-15 08:18:58.892][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-15 08:18:58.893][self$setPropertyValue]
biodb.DEBUG[2022-10-15 08:18:58.894][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2022-10-15 08:18:58.895][self$setPropertyValue]
biodb.DEBUG[2022-10-15 08:18:58.896][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2022-10-15 08:18:58.896][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-15 08:18:58.897][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-15 08:18:58.898][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-15 08:18:58.899][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-15 08:18:58.900][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-15 08:18:58.900][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-15 08:18:58.901][self$setPropertyValue]
biodb.DEBUG[2022-10-15 08:18:58.902][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-15 08:18:58.903][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-15 08:18:58.904][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2022-10-15 08:18:58.904][self$setPropertyValue]
biodb.DEBUG[2022-10-15 08:18:58.905][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-10-15 08:18:58.906][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:18:58.907][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:18:58.908][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:18:58.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:18:58.909][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:18:58.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:18:58.911][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:18:58.911][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:18:58.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:18:58.913][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:18:58.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:18:58.914][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:18:58.915][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:18:58.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:18:58.917][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:18:58.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:18:58.918][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:18:58.919][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:18:58.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:18:58.920][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:18:58.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:18:58.922][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:18:58.922][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:18:58.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:18:58.924][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:18:58.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:18:58.925][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:18:58.926][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:18:58.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:18:58.927][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:18:58.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:18:58.929][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.DEBUG[2022-10-15 08:18:58.930][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:18:58.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:18:58.931][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:18:58.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:18:58.933][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:18:58.933][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:18:58.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:18:58.935][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:18:58.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:18:58.936][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:18:58.937][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:18:58.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:18:58.939][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:18:58.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:18:58.940][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:18:58.941][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:18:58.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:18:58.945][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:18:58.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:18:58.946][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:18:58.947][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:18:58.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:18:58.949][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:18:58.949][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:18:58.950][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:18:58.951][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:18:58.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:18:58.952][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:18:58.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:18:58.954][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:18:58.955][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:18:58.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:18:58.956][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:18:58.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:18:58.957][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:18:58.958][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:18:58.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:18:58.960][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:18:58.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:18:58.961][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:18:58.962][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:18:58.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:18:58.963][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:18:58.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:18:58.965][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[2022-10-15 08:18:58.966][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:18:58.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:18:58.967][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:18:58.968][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:18:58.969][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:18:58.969][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:18:58.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:18:58.971][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:18:58.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:18:58.972][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:18:58.973][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2022-10-15 08:18:58.974][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2022-10-15 08:18:58.976][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2022-10-15 08:18:58.977][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2022-10-15 08:18:58.978][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2022-10-15 08:18:58.979][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2022-10-15 08:18:58.980][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2022-10-15 08:18:58.981][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2022-10-15 08:18:58.982][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2022-10-15 08:18:58.983][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2022-10-15 08:18:58.984][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2022-10-15 08:18:58.986][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2022-10-15 08:18:58.987][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2022-10-15 08:18:58.988][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2022-10-15 08:18:58.989][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2022-10-15 08:18:58.990][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2022-10-15 08:18:58.991][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2022-10-15 08:18:58.992][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2022-10-15 08:18:58.994][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2022-10-15 08:18:58.995][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2022-10-15 08:18:58.996][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2022-10-15 08:18:58.997][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2022-10-15 08:18:58.998][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2022-10-15 08:18:58.999][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2022-10-15 08:18:59.000][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2022-10-15 08:18:59.002][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2022-10-15 08:18:59.003][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2022-10-15 08:18:59.004][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2022-10-15 08:18:59.005][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2022-10-15 08:18:59.006][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2022-10-15 08:18:59.007][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2022-10-15 08:18:59.008][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2022-10-15 08:18:59.010][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2022-10-15 08:18:59.011][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2022-10-15 08:18:59.012][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2022-10-15 08:18:59.013][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2022-10-15 08:18:59.014][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2022-10-15 08:18:59.015][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2022-10-15 08:18:59.016][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2022-10-15 08:18:59.017][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2022-10-15 08:18:59.019][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2022-10-15 08:18:59.020][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2022-10-15 08:18:59.021][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2022-10-15 08:18:59.022][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2022-10-15 08:18:59.023][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2022-10-15 08:18:59.024][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2022-10-15 08:18:59.025][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2022-10-15 08:18:59.027][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2022-10-15 08:18:59.028][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2022-10-15 08:18:59.029][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2022-10-15 08:18:59.030][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2022-10-15 08:18:59.031][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2022-10-15 08:18:59.032][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2022-10-15 08:18:59.033][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2022-10-15 08:18:59.035][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2022-10-15 08:18:59.036][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2022-10-15 08:18:59.037][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2022-10-15 08:18:59.038][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2022-10-15 08:18:59.039][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2022-10-15 08:18:59.040][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2022-10-15 08:18:59.041][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2022-10-15 08:18:59.043][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2022-10-15 08:18:59.044][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2022-10-15 08:18:59.045][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2022-10-15 08:18:59.047][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2022-10-15 08:18:59.049][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2022-10-15 08:18:59.051][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2022-10-15 08:18:59.053][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2022-10-15 08:18:59.054][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2022-10-15 08:18:59.056][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2022-10-15 08:18:59.058][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2022-10-15 08:18:59.061][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2022-10-15 08:18:59.064][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2022-10-15 08:18:59.066][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2022-10-15 08:18:59.067][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2022-10-15 08:18:59.069][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2022-10-15 08:18:59.071][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2022-10-15 08:18:59.073][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2022-10-15 08:18:59.074][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2022-10-15 08:18:59.076][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2022-10-15 08:18:59.078][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2022-10-15 08:18:59.079][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2022-10-15 08:18:59.081][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2022-10-15 08:18:59.083][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2022-10-15 08:18:59.085][initialize] This is biodb version 1.4.2.
biodb.DEBUG[2022-10-15 08:18:59.086][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2022-10-15 08:18:59.087][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:18:59.088][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:18:59.089][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:18:59.090][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:18:59.091][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:18:59.092][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:18:59.093][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:18:59.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:18:59.095][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:18:59.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:18:59.096][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:18:59.097][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:18:59.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:18:59.099][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:18:59.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:18:59.101][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:18:59.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:18:59.103][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:18:59.104][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:18:59.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:18:59.106][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:18:59.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:18:59.108][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:18:59.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:18:59.110][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:18:59.111][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:18:59.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:18:59.112][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:18:59.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:18:59.114][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:18:59.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:18:59.116][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:18:59.117][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:18:59.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:18:59.119][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:18:59.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:18:59.121][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:18:59.122][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:18:59.123][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:18:59.124][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:18:59.125][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:18:59.126][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:18:59.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:18:59.128][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:18:59.129][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:18:59.130][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:18:59.131][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:18:59.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:18:59.133][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:18:59.134][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:18:59.135][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:18:59.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:18:59.137][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:18:59.138][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:18:59.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:18:59.140][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:18:59.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:18:59.142][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:18:59.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:18:59.144][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:18:59.145][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:18:59.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:18:59.147][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:18:59.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:18:59.149][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:18:59.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:18:59.151][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:18:59.151][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:18:59.152][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:18:59.153][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:18:59.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:18:59.155][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:18:59.156][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:18:59.157][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:18:59.158][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:18:59.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:18:59.160][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:18:59.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:18:59.162][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:18:59.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:18:59.164][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:18:59.165][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:18:59.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:18:59.167][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:18:59.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:18:59.169][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:18:59.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:18:59.170][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:18:59.171][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:18:59.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:18:59.173][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:18:59.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:18:59.175][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:18:59.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:18:59.177][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:18:59.178][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:18:59.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:18:59.180][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:18:59.181][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:18:59.182][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:18:59.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:18:59.183][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:18:59.184][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:18:59.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:18:59.186][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:18:59.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:18:59.188][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:18:59.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:18:59.190][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2022-10-15 08:18:59.191][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:18:59.192][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:18:59.193][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:18:59.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:18:59.194][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:18:59.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:18:59.196][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[2022-10-15 08:18:59.197][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2022-10-15 08:18:59.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:18:59.199][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:18:59.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:18:59.200][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:18:59.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:18:59.202][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[2022-10-15 08:18:59.204][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.15-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2022-10-15 08:18:59.205][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2022-10-15 08:18:59.207][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2022-10-15 08:18:59.208][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2022-10-15 08:18:59.209][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2022-10-15 08:18:59.210][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2022-10-15 08:18:59.211][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2022-10-15 08:18:59.213][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2022-10-15 08:18:59.214][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2022-10-15 08:18:59.215][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2022-10-15 08:18:59.216][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2022-10-15 08:18:59.217][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2022-10-15 08:18:59.218][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2022-10-15 08:18:59.219][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2022-10-15 08:18:59.220][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2022-10-15 08:18:59.220][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2022-10-15 08:18:59.220][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2022-10-15 08:18:59.220][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2022-10-15 08:18:59.220][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2022-10-15 08:18:59.220][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2022-10-15 08:18:59.220][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2022-10-15 08:18:59.220][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2022-10-15 08:18:59.221][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2022-10-15 08:18:59.223][self$setPropertyValue]
biodb.DEBUG[2022-10-15 08:18:59.224][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2022-10-15 08:18:59.225][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-15 08:18:59.226][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-15 08:18:59.227][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2022-10-15 08:18:59.227][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2022-10-15 08:18:59.228][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2022-10-15 08:18:59.229][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2022-10-15 08:18:59.230][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2022-10-15 08:18:59.230][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2022-10-15 08:18:59.230][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2022-10-15 08:18:59.230][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2022-10-15 08:18:59.231][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2022-10-15 08:18:59.232][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2022-10-15 08:18:59.233][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2022-10-15 08:18:59.234][self$setPropertyValue]
biodb.DEBUG[2022-10-15 08:18:59.235][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2022-10-15 08:18:59.238][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2022-10-15 08:18:59.239][super$initialize] Register connector nci.cactus with the request scheduler
biodb.DEBUG[2022-10-15 08:18:59.241][private$bdb$getRequestScheduler()$re ...] Register connector nci.cactus.
biodb.DEBUG[2022-10-15 08:18:59.242][private$addConnectorRules] Create new rule for URL "cactus.nci.nih.gov" of connector "nci.cactus".
biodb.DEBUG[2022-10-15 08:18:59.243][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2022-10-15 08:18:59.244][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2022-10-15 08:18:59.246][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2022-10-15 08:18:59.247][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2022-10-15 08:18:59.248][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2022-10-15 08:18:59.249][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2022-10-15 08:18:59.250][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2022-10-15 08:18:59.252][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector nci.cactus from the request scheduler
biodb.INFO [2022-10-15 08:18:59.253][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2022-10-15 08:18:59.254][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2022-10-15 08:18:59.254][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2022-10-15 08:18:59.255][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2022-10-15 08:18:59.256][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2022-10-15 08:18:59.257][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2022-10-15 08:18:59.258][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2022-10-15 08:18:59.259][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 92 ]
> 
> proc.time()
   user  system elapsed 
514.218  39.271 584.082

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNci_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc-longtests/meat/biodbNci.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘biodbNci/DESCRIPTION’ ... OK
* this is package ‘biodbNci’ version ‘1.0.0’
* 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 ‘biodbNci’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
  Running ‘testthat.R’
 OK
* DONE

Status: OK

Installation output

biodbNci.Rcheck/00install.out

* installing *source* package ‘biodbNci’ ...
** using staged installation
** libs
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/testthat/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/testthat/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c extractEntries.cpp -o extractEntries.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/testthat/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c test-100-example.cpp -o test-100-example.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/testthat/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c test-runner.cpp -o test-runner.o
g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.15-bioc/R/lib -L/usr/local/lib -o biodbNci.so RcppExports.o extractEntries.o test-100-example.o test-runner.o -L/home/biocbuild/bbs-3.15-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.15-bioc-longtests/meat/biodbNci.Rcheck/00LOCK-biodbNci/00new/biodbNci/libs
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (biodbNci)