Back to Long Tests report for BioC 3.20

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

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4672
palomino4Windows Server 2022 Datacenterx644.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 4407
merida1macOS 12.7.4 Montereyx86_644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4434
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 11/32HostnameOS / ArchCHECK
biodbNci 1.9.0  (landing page)
Pierrick Roger
Snapshot Date: 2024-06-08 09:55 -0400 (Sat, 08 Jun 2024)
git_url: https://git.bioconductor.org/packages/biodbNci
git_branch: devel
git_last_commit: 12acfea
git_last_commit_date: 2024-04-30 11:41:04 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK  
palomino4Windows Server 2022 Datacenter / x64  ERROR  
merida1macOS 12.7.4 Monterey / x86_64  OK  

CHECK results for biodbNci on merida1

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

raw results


Summary

Package: biodbNci
Version: 1.9.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNci_1.9.0.tar.gz
StartedAt: 2024-06-08 16:02:30 -0400 (Sat, 08 Jun 2024)
EndedAt: 2024-06-08 16:33:08 -0400 (Sat, 08 Jun 2024)
EllapsedTime: 1838.5 seconds
RetCode: 0
Status:   OK  
CheckDir: biodbNci.Rcheck
Warnings: 0

Tests output

biodbNci.Rcheck/tests/testthat.Rout


R version 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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

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Type 'contributors()' for more information and
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Type 'demo()' for some demos, 'help()' for on-line help, or
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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbNci)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbNci")
biodb.INFO [2024-06-08 16:03:45.329][biodb::testContext]
biodb.INFO [2024-06-08 16:03:45.333][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-08 16:03:45.334][biodb::testContext] Test context - Generic long tests
biodb.INFO [2024-06-08 16:03:45.336][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-08 16:03:45.337][biodb::testContext]
biodb.INFO [2024-06-08 16:03:45.344][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.13.0.
biodb.DEBUG[2024-06-08 16:03:45.346][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-06-08 16:03:45.353][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-08 16:03:45.355][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-06-08 16:03:45.356][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-06-08 16:03:45.357][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:03:45.358][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:03:45.359][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:03:45.360][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-06-08 16:03:45.385][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-06-08 16:03:45.386][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:03:45.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:03:45.389][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:03:45.390][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-06-08 16:03:45.391][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-06-08 16:03:45.392][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:03:45.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:03:45.394][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:03:45.396][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-06-08 16:03:45.397][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-06-08 16:03:45.398][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-06-08 16:03:45.399][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:03:45.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:03:45.401][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:03:45.403][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-06-08 16:03:45.404][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-06-08 16:03:45.405][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-06-08 16:03:45.406][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:03:45.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:03:45.408][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:03:45.409][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-06-08 16:03:45.411][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-06-08 16:03:45.412][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:03:45.413][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:03:45.414][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:03:45.415][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-06-08 16:03:45.416][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-06-08 16:03:45.418][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-06-08 16:03:45.419][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:03:45.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:03:45.421][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:03:45.422][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-06-08 16:03:45.423][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-06-08 16:03:45.424][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:03:45.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:03:45.427][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:03:45.428][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-06-08 16:03:45.429][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-06-08 16:03:45.430][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-06-08 16:03:45.431][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:03:45.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:03:45.433][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:03:45.435][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-06-08 16:03:45.436][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-06-08 16:03:45.437][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-06-08 16:03:45.438][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-06-08 16:03:45.440][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-06-08 16:03:45.441][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-06-08 16:03:45.443][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:03:45.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:03:45.445][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:03:45.446][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-06-08 16:03:45.448][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-06-08 16:03:45.449][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:03:45.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:03:45.451][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:03:45.452][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-06-08 16:03:45.453][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-06-08 16:03:45.455][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:03:45.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:03:45.457][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:03:45.458][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-06-08 16:03:45.459][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-06-08 16:03:45.460][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:03:45.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:03:45.463][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:03:45.464][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-06-08 16:03:45.465][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-06-08 16:03:45.466][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:03:45.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:03:45.468][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:03:45.470][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-06-08 16:03:45.471][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-06-08 16:03:45.472][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:03:45.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:03:45.474][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:03:45.476][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-06-08 16:03:45.477][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-06-08 16:03:45.487][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-06-08 16:03:45.489][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:03:45.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:03:45.491][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:03:45.492][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-06-08 16:03:45.493][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-06-08 16:03:45.495][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-06-08 16:03:45.496][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:03:45.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:03:45.498][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:03:45.502][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-06-08 16:03:45.548][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-08 16:03:45.576][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-06-08 16:03:45.577][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-08 16:03:45.578][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-08 16:03:45.580][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-08 16:03:45.581][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-08 16:03:45.582][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-08 16:03:45.583][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-08 16:03:45.585][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-08 16:03:45.586][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-08 16:03:45.587][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-08 16:03:45.588][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-06-08 16:03:45.590][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-08 16:03:45.591][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:03:45.592][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-08 16:03:45.593][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-08 16:03:45.593][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-08 16:03:45.593][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-08 16:03:45.593][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-08 16:03:45.593][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-08 16:03:45.595][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-08 16:03:45.596][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-08 16:03:45.597][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-08 16:03:45.598][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-08 16:03:45.599][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-08 16:03:45.600][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-08 16:03:45.602][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-08 16:03:45.603][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:03:45.604][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-08 16:03:45.605][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-08 16:03:45.606][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-08 16:03:45.608][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:03:45.609][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-06-08 16:03:45.611][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-08 16:03:45.613][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-06-08 16:03:45.614][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-08 16:03:45.615][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-08 16:03:45.616][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-08 16:03:45.618][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-08 16:03:45.619][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-08 16:03:45.620][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-08 16:03:45.621][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-08 16:03:45.623][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-08 16:03:45.624][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-08 16:03:45.625][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-06-08 16:03:45.627][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-08 16:03:45.628][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:03:45.629][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-08 16:03:45.630][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-08 16:03:45.630][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-08 16:03:45.630][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-08 16:03:45.630][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-08 16:03:45.630][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-08 16:03:45.632][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-08 16:03:45.633][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-08 16:03:45.634][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-08 16:03:45.635][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-08 16:03:45.636][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-08 16:03:45.637][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-08 16:03:45.639][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-08 16:03:45.640][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:03:45.641][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-08 16:03:45.642][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-08 16:03:45.643][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-08 16:03:45.644][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:03:45.646][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-06-08 16:03:45.648][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-08 16:03:45.649][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-06-08 16:03:45.651][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-08 16:03:45.652][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-08 16:03:45.653][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-08 16:03:45.654][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-08 16:03:45.656][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-08 16:03:45.657][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-08 16:03:45.658][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-08 16:03:45.659][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-08 16:03:45.661][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-08 16:03:45.662][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-06-08 16:03:45.663][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-08 16:03:45.664][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:03:45.665][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-08 16:03:45.667][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:03:45.668][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-08 16:03:45.669][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-08 16:03:45.670][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-08 16:03:45.671][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-08 16:03:45.673][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-08 16:03:45.674][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-08 16:03:45.675][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-08 16:03:45.676][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:03:45.677][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-08 16:03:45.678][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-08 16:03:45.680][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-08 16:03:45.681][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:03:45.682][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-06-08 16:03:45.684][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-08 16:03:45.686][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-06-08 16:03:45.687][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-08 16:03:45.688][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-08 16:03:45.689][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-08 16:03:45.691][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-08 16:03:45.692][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-08 16:03:45.693][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-08 16:03:45.694][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-08 16:03:45.696][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-08 16:03:45.697][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-08 16:03:45.698][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-06-08 16:03:45.699][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-08 16:03:45.701][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:03:45.702][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-08 16:03:45.703][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:03:45.704][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-08 16:03:45.705][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-08 16:03:45.707][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-08 16:03:45.708][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-08 16:03:45.709][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-08 16:03:45.710][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-08 16:03:45.711][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-08 16:03:45.712][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:03:45.714][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-08 16:03:45.715][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-08 16:03:45.716][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-08 16:03:45.717][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:03:45.722][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-08 16:03:45.723][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:03:45.724][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:03:45.725][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:03:45.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:03:45.727][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:03:45.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:03:45.730][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:03:45.731][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:03:45.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:03:45.733][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:03:45.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:03:45.736][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:03:45.737][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:03:45.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:03:45.739][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:03:45.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:03:45.741][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:03:45.742][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:03:45.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:03:45.745][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:03:45.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:03:45.747][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:03:45.748][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:03:45.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:03:45.750][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:03:45.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:03:45.752][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:03:45.754][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:03:45.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:03:45.756][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:03:45.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:03:45.758][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:03:45.759][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:03:45.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:03:45.761][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:03:45.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:03:45.764][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:03:45.765][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:03:45.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:03:45.767][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:03:45.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:03:45.769][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:03:45.770][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:03:45.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:03:45.773][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:03:45.774][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:03:45.775][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:03:45.776][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:03:45.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:03:45.778][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:03:45.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:03:45.781][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:03:45.787][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:03:45.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:03:45.789][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:03:45.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:03:45.791][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:03:45.792][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:03:45.793][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:03:45.794][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:03:45.796][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:03:45.797][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:03:45.798][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:03:45.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:03:45.800][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:03:45.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:03:45.802][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:03:45.803][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:03:45.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:03:45.805][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:03:45.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:03:45.808][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:03:45.809][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:03:45.810][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:03:45.811][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:03:45.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:03:45.813][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:03:45.814][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:03:45.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:03:45.816][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:03:45.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:03:45.819][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:03:45.820][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:03:45.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:03:45.822][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:03:45.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:03:45.824][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:03:45.825][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-06-08 16:03:45.830][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-06-08 16:03:45.832][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-06-08 16:03:45.834][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-06-08 16:03:45.836][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-08 16:03:45.838][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-08 16:03:45.840][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-06-08 16:03:45.841][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-06-08 16:03:45.843][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-08 16:03:45.845][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-08 16:03:45.847][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-08 16:03:45.849][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-06-08 16:03:45.850][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-06-08 16:03:45.852][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-06-08 16:03:45.854][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-06-08 16:03:45.855][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-08 16:03:45.857][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-06-08 16:03:45.859][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-06-08 16:03:45.860][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-08 16:03:45.862][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-06-08 16:03:45.864][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-06-08 16:03:45.866][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-06-08 16:03:45.867][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-06-08 16:03:45.869][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-06-08 16:03:45.871][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-06-08 16:03:45.873][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-06-08 16:03:45.875][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-06-08 16:03:45.876][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-06-08 16:03:45.878][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-06-08 16:03:45.880][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-06-08 16:03:45.882][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-06-08 16:03:45.883][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-06-08 16:03:45.885][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-06-08 16:03:45.887][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-06-08 16:03:45.888][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-06-08 16:03:45.890][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-06-08 16:03:45.892][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-06-08 16:03:45.894][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-06-08 16:03:45.895][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-06-08 16:03:45.897][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-06-08 16:03:45.899][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-06-08 16:03:45.901][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-06-08 16:03:45.902][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-06-08 16:03:45.904][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-06-08 16:03:45.906][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-06-08 16:03:45.908][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-06-08 16:03:45.909][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-06-08 16:03:45.911][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-06-08 16:03:45.913][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-06-08 16:03:45.914][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-06-08 16:03:45.916][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-06-08 16:03:45.918][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-06-08 16:03:45.920][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-06-08 16:03:45.921][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-06-08 16:03:45.923][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-06-08 16:03:45.925][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-06-08 16:03:45.926][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-06-08 16:03:45.928][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-06-08 16:03:45.930][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-06-08 16:03:45.932][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-06-08 16:03:45.933][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-06-08 16:03:45.935][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-06-08 16:03:45.937][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-06-08 16:03:45.938][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-06-08 16:03:45.940][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-06-08 16:03:45.942][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-06-08 16:03:45.944][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-08 16:03:45.945][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-08 16:03:45.947][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-06-08 16:03:45.949][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-06-08 16:03:45.950][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-06-08 16:03:45.952][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-06-08 16:03:45.954][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-06-08 16:03:45.955][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-06-08 16:03:45.957][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-06-08 16:03:45.959][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-06-08 16:03:45.961][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-06-08 16:03:45.962][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-06-08 16:03:45.964][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-06-08 16:03:45.966][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-06-08 16:03:45.967][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-06-08 16:03:45.969][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-06-08 16:03:45.971][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-06-08 16:03:45.978][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-06-08 16:03:45.980][initialize] This is biodb version 1.13.0.
biodb.DEBUG[2024-06-08 16:03:45.984][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-08 16:03:45.985][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:03:45.986][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:03:45.987][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:03:45.988][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:03:45.994][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:03:45.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:03:45.997][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:03:45.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:03:45.999][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:03:46.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:03:46.001][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:03:46.002][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:03:46.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:03:46.004][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:03:46.006][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:03:46.007][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:03:46.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:03:46.014][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:03:46.015][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:03:46.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:03:46.017][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:03:46.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:03:46.019][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:03:46.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:03:46.021][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:03:46.022][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:03:46.023][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:03:46.024][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:03:46.025][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:03:46.026][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:03:46.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:03:46.029][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:03:46.030][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:03:46.031][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:03:46.032][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:03:46.033][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:03:46.034][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:03:46.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:03:46.036][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:03:46.037][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:03:46.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:03:46.039][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:03:46.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:03:46.041][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:03:46.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:03:46.044][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:03:46.045][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:03:46.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:03:46.047][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:03:46.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:03:46.049][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:03:46.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:03:46.051][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:03:46.052][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:03:46.053][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:03:46.054][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:03:46.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:03:46.057][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:03:46.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:03:46.059][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:03:46.060][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:03:46.061][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:03:46.062][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:03:46.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:03:46.064][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:03:46.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:03:46.066][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:03:46.067][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:03:46.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:03:46.069][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:03:46.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:03:46.072][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:03:46.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:03:46.074][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:03:46.075][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:03:46.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:03:46.077][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:03:46.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:03:46.079][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:03:46.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:03:46.081][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:03:46.082][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:03:46.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:03:46.085][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:03:46.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:03:46.087][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:03:46.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:03:46.089][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:03:46.090][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:03:46.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:03:46.092][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:03:46.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:03:46.094][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:03:46.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:03:46.097][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:03:46.098][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:03:46.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:03:46.100][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:03:46.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:03:46.102][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:03:46.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:03:46.104][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:03:46.105][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:03:46.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:03:46.108][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:03:46.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:03:46.110][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:03:46.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:03:46.112][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:03:46.113][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:03:46.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:03:46.115][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:03:46.116][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:03:46.118][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:03:46.119][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:03:46.120][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:03:46.121][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:03:46.122][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:03:46.123][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:03:46.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:03:46.125][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:03:46.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:03:46.127][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:03:46.130][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2024-06-08 16:03:46.143][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2024-06-08 16:03:46.145][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-08 16:03:46.166][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2024-06-08 16:03:46.168][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-08 16:03:46.169][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-08 16:03:46.170][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2024-06-08 16:03:46.172][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2024-06-08 16:03:46.173][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-06-08 16:03:46.174][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-08 16:03:46.175][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2024-06-08 16:03:46.176][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-08 16:03:46.178][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-08 16:03:46.179][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2024-06-08 16:03:46.180][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-08 16:03:46.181][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2024-06-08 16:03:46.181][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2024-06-08 16:03:46.181][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2024-06-08 16:03:46.181][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2024-06-08 16:03:46.181][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2024-06-08 16:03:46.181][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2024-06-08 16:03:46.181][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2024-06-08 16:03:46.183][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-06-08 16:03:46.184][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:03:46.185][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-06-08 16:03:46.187][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-08 16:03:46.188][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-08 16:03:46.189][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-08 16:03:46.190][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-08 16:03:46.191][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-08 16:03:46.192][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-08 16:03:46.194][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2024-06-08 16:03:46.194][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2024-06-08 16:03:46.194][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2024-06-08 16:03:46.194][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2024-06-08 16:03:46.195][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-08 16:03:46.196][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-08 16:03:46.197][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-06-08 16:03:46.198][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:03:46.206][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2024-06-08 16:03:46.230][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2024-06-08 16:03:46.256][super$initialize] Register connector nci.cactus with the request scheduler
biodb.DEBUG[2024-06-08 16:03:46.260][private$bdb$getRequestScheduler()$re ...] Register connector nci.cactus.
biodb.DEBUG[2024-06-08 16:03:46.264][private$addConnectorRules] Create new rule for URL "cactus.nci.nih.gov" of connector "nci.cactus".
biodb.DEBUG[2024-06-08 16:03:46.268][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-08 16:03:46.270][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-08 16:03:46.271][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-06-08 16:03:46.273][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-06-08 16:03:46.274][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-06-08 16:03:46.280][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2024-06-08 16:03:46.290][biodb::testThat]
biodb.INFO [2024-06-08 16:03:46.292][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-06-08 16:03:46.293][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-08 16:03:46.294][biodb::testThat]
biodb.TRACE[2024-06-08 16:03:46.298][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-749674-content.sdf".
biodb.DEBUG[2024-06-08 16:03:46.300][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2024-06-08 16:03:46.304][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2024-06-08 16:03:46.313][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-08 16:03:46.315][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:03:46.316][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:03:46.331][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:03:46.333][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:03:46.334][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:03:46.335][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-08 16:03:46.357][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:03:46.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:03:46.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:46.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:46.363][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:03:46.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:03:46.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:46.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:46.386][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-08 16:03:46.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-08 16:03:46.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:46.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:46.428][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-08 16:03:46.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-08 16:03:46.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:46.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:46.434][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-08 16:03:46.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-08 16:03:46.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:46.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:46.439][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-08 16:03:46.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-08 16:03:46.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:46.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:46.446][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-08 16:03:46.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-08 16:03:46.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:46.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:46.451][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-08 16:03:46.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-08 16:03:46.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:46.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:46.457][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-08 16:03:46.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-08 16:03:46.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:46.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:46.462][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-08 16:03:46.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-08 16:03:46.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:46.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:46.468][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:03:46.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:03:46.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:46.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:46.473][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:03:46.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:03:46.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:46.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:46.478][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:03:46.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:03:46.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:46.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:46.483][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:03:46.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:03:46.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:46.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:46.488][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:03:46.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:03:46.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:46.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:46.501][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:03:46.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:03:46.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:46.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:46.506][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:03:46.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:03:46.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:46.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:46.557][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:03:46.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:03:46.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:46.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:46.562][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:03:46.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:03:46.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:46.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:46.567][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:03:46.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:03:46.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:46.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-08 16:03:46.572][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 749674.
biodb.TRACE[2024-06-08 16:03:46.575][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-08 16:03:46.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-08 16:03:46.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:46.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:46.580][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-08 16:03:46.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-08 16:03:46.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:46.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:46.585][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-08 16:03:46.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-08 16:03:46.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:46.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:46.589][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-08 16:03:46.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-08 16:03:46.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:46.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:46.611][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:03:46.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:03:46.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:46.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:46.633][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:03:46.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:03:46.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:46.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:46.643][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:03:46.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:03:46.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:46.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:46.648][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:03:46.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:03:46.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:46.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:46.653][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:03:46.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:03:46.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:46.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:46.660][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:03:46.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:03:46.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:46.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:46.665][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:03:46.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:03:46.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:46.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:46.670][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:03:46.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:03:46.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:46.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:46.675][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:03:46.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:03:46.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:46.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:46.685][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:03:46.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:03:46.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:46.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:46.690][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:03:46.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:03:46.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:46.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:46.703][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:03:46.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:03:46.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:46.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:46.708][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:03:46.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:03:46.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:46.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:46.713][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:03:46.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:03:46.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:46.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:46.718][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:03:46.720][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:03:46.721][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:46.722][ef$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:46.723][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:03:46.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:03:46.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:46.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:46.739][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-08 16:03:46.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-08 16:03:46.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:46.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:46.744][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-08 16:03:46.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-08 16:03:46.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:46.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:46.749][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-08 16:03:46.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-08 16:03:46.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:46.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:46.754][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-08 16:03:46.755][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-08 16:03:46.757][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:46.758][ef$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:46.759][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-08 16:03:46.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-08 16:03:46.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:46.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:46.774][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-08 16:03:46.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-08 16:03:46.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:46.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:46.780][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-08 16:03:46.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-08 16:03:46.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:46.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:46.785][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-08 16:03:46.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-08 16:03:46.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:46.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:46.790][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-08 16:03:46.791][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-08 16:03:46.792][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:46.794][ef$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:46.795][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-08 16:03:46.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-08 16:03:46.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:46.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:46.810][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-08 16:03:46.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-08 16:03:46.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:46.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:46.816][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-08 16:03:46.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-08 16:03:46.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:46.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:46.821][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-08 16:03:46.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-08 16:03:46.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:46.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:46.826][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-08 16:03:46.827][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-08 16:03:46.828][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:46.829][ef$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:46.831][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-08 16:03:46.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-08 16:03:46.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:46.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:46.846][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-08 16:03:46.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-08 16:03:46.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:46.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:46.851][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-08 16:03:46.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-08 16:03:46.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:46.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:46.856][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-08 16:03:46.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-08 16:03:46.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:46.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:46.861][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-08 16:03:46.862][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-08 16:03:46.863][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:46.864][ef$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:46.866][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-08 16:03:46.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-08 16:03:46.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:46.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:46.885][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:03:46.886][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:03:46.888][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:46.889][ef$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:46.895][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-08 16:03:46.896][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-08 16:03:46.897][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:46.899][ef$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:46.905][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-08 16:03:46.906][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-08 16:03:46.907][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:46.909][ef$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:46.915][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-08 16:03:46.916][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-08 16:03:46.917][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:46.919][ef$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:46.925][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-08 16:03:46.926][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-08 16:03:46.928][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:46.929][ef$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:46.952][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-750690-content.sdf".
biodb.DEBUG[2024-06-08 16:03:47.002][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2024-06-08 16:03:47.003][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2024-06-08 16:03:47.005][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-08 16:03:47.006][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:03:47.007][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:03:47.014][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:03:47.015][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:03:47.016][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:03:47.017][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-08 16:03:47.032][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:03:47.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:03:47.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:47.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:47.038][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:03:47.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:03:47.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:47.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:47.072][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-08 16:03:47.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-08 16:03:47.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:47.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:47.077][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-08 16:03:47.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-08 16:03:47.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:47.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:47.083][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-08 16:03:47.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-08 16:03:47.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:47.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:47.088][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-08 16:03:47.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-08 16:03:47.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:47.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:47.094][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-08 16:03:47.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-08 16:03:47.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:47.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:47.099][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-08 16:03:47.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-08 16:03:47.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:47.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:47.104][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:03:47.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:03:47.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:47.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:47.109][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:03:47.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:03:47.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:47.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:47.115][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:03:47.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:03:47.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:47.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:47.120][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:03:47.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:03:47.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:47.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:47.125][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:03:47.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:03:47.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:47.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:47.130][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:03:47.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:03:47.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:47.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:47.135][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:03:47.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:03:47.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:47.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:47.142][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-08 16:03:47.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-08 16:03:47.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:47.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:47.147][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-08 16:03:47.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-08 16:03:47.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:47.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:47.152][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-08 16:03:47.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-08 16:03:47.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:47.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:47.157][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-08 16:03:47.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-08 16:03:47.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:47.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:47.164][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:03:47.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:03:47.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:47.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:47.169][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:03:47.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:03:47.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:47.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:47.174][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:03:47.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:03:47.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:47.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:47.179][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:03:47.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:03:47.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:47.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:47.184][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:03:47.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:03:47.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:47.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:47.189][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:03:47.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:03:47.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:47.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:47.194][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:03:47.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:03:47.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:47.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:47.199][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:03:47.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:03:47.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:47.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:47.205][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:03:47.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:03:47.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:47.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:47.210][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:03:47.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:03:47.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:47.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-08 16:03:47.215][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 750690.
biodb.TRACE[2024-06-08 16:03:47.247][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-08 16:03:47.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-08 16:03:47.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:47.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:47.252][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-08 16:03:47.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-08 16:03:47.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:47.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:47.257][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-08 16:03:47.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-08 16:03:47.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:47.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:47.263][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-08 16:03:47.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-08 16:03:47.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:47.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:47.269][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:03:47.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:03:47.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:47.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:47.279][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:03:47.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:03:47.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:47.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:47.290][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:03:47.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:03:47.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:47.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:47.296][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:03:47.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:03:47.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:47.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:47.301][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:03:47.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:03:47.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:47.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:47.308][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:03:47.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:03:47.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:47.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:47.313][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:03:47.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:03:47.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:47.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:47.318][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:03:47.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:03:47.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:47.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:47.323][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:03:47.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:03:47.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:47.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:47.328][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:03:47.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:03:47.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:47.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:47.333][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:03:47.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:03:47.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:47.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:47.360][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:03:47.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:03:47.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:47.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:47.365][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:03:47.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:03:47.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:47.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:47.370][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:03:47.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:03:47.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:47.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:47.375][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:03:47.376][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:03:47.378][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:47.379][ef$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:47.380][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:03:47.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:03:47.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:47.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:47.395][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-08 16:03:47.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-08 16:03:47.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:47.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:47.400][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-08 16:03:47.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-08 16:03:47.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:47.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:47.405][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-08 16:03:47.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-08 16:03:47.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:47.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:47.410][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-08 16:03:47.411][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-08 16:03:47.412][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:47.414][ef$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:47.415][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-08 16:03:47.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-08 16:03:47.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:47.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:47.430][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:03:47.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:03:47.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:47.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:47.439][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:03:47.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:03:47.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:47.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:47.444][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:03:47.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:03:47.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:47.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:47.449][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:03:47.450][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:03:47.452][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:47.453][ef$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:47.454][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:03:47.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:03:47.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:47.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:47.468][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-08 16:03:47.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-08 16:03:47.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:47.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:47.473][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-08 16:03:47.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-08 16:03:47.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:47.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:47.478][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-08 16:03:47.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-08 16:03:47.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:47.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:47.483][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-08 16:03:47.484][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-08 16:03:47.485][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:47.487][ef$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:47.488][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-08 16:03:47.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-08 16:03:47.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:47.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:47.502][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-08 16:03:47.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-08 16:03:47.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:47.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:47.508][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-08 16:03:47.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-08 16:03:47.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:47.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:47.512][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-08 16:03:47.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-08 16:03:47.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:47.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:47.517][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-08 16:03:47.519][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-08 16:03:47.520][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:47.521][ef$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:47.522][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-08 16:03:47.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-08 16:03:47.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:47.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:47.537][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-08 16:03:47.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-08 16:03:47.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:47.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:47.542][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-08 16:03:47.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-08 16:03:47.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:47.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:47.547][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-08 16:03:47.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-08 16:03:47.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:47.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:47.552][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-08 16:03:47.554][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-08 16:03:47.555][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:47.556][ef$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:47.557][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-08 16:03:47.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-08 16:03:47.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:47.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:47.572][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-08 16:03:47.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-08 16:03:47.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:47.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:47.578][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-08 16:03:47.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-08 16:03:47.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:47.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:47.583][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-08 16:03:47.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-08 16:03:47.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:47.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:47.588][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-08 16:03:47.589][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-08 16:03:47.590][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:47.592][ef$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:47.593][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-08 16:03:47.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-08 16:03:47.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:47.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:47.608][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:03:47.609][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:03:47.611][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:47.612][ef$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:47.618][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-08 16:03:47.620][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-08 16:03:47.621][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:47.622][ef$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:47.633][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-08 16:03:47.634][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-08 16:03:47.636][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:47.637][ef$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:47.643][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-08 16:03:47.645][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-08 16:03:47.646][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:47.647][ef$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:47.653][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-08 16:03:47.655][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-08 16:03:47.656][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:47.657][ef$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:47.663][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-08 16:03:47.665][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-08 16:03:47.666][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:47.667][ef$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:03:47.674][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:03:47.675][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:03:47.676][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:03:47.677][ef$get] fields variable is a list.
biodb.INFO [2024-06-08 16:03:47.688][biodb::testThat]
biodb.INFO [2024-06-08 16:03:47.689][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-06-08 16:03:47.690][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-08 16:03:47.691][biodb::testThat]
biodb.DEBUG[2024-06-08 16:03:47.694][private$loadEntries] Creating entries from ids [2]: "749674, 750690".
biodb.DEBUG[2024-06-08 16:03:47.701][conn$getEntryContent] Get NCI CACTUS entry content(s) for 2 id(s)...
biodb.INFO [2024-06-08 16:03:47.706][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427" for "nci.cactus-8efc65070d01b214e760b1d4932ee427".
biodb.DEBUG[2024-06-08 16:03:47.708][self$isDownloaded] Database nci.cactus has not yet been downloaded.
biodb.INFO [2024-06-08 16:03:47.709][self$download] Downloading whole database of nci.cactus.
biodb.INFO [2024-06-08 16:03:47.710][private$doDownload] Downloading NCI CACTUS database at "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz" ...
biodb.DEBUG[2024-06-08 16:03:47.712][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[2024-06-08 16:03:50.441][cch$addFilesToCache] Moving files to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/nci.cactusfd461723cf5cgz".
biodb.TRACE[2024-06-08 16:03:50.443][private$doAddFilesToCache] Destination files are [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/download.gz".
biodb.DEBUG[2024-06-08 16:03:50.445][cch$addFilesToCache] Done adding files.
biodb.DEBUG[2024-06-08 16:03:50.446][self$getDownloadPath] Download path of nci.cactus is "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/download.gz".
biodb.DEBUG[2024-06-08 16:03:50.448][self$download] Downloading of nci.cactus completed.
biodb.TRACE[2024-06-08 16:03:50.450][self$addFilesToCache] Moving files to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/markerfd463002ace2marker".
biodb.TRACE[2024-06-08 16:03:50.452][private$doAddFilesToCache] Destination files are [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/downloaded.marker".
biodb.DEBUG[2024-06-08 16:03:50.453][self$addFilesToCache] Done adding files.
biodb.DEBUG[2024-06-08 16:03:50.455][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.INFO [2024-06-08 16:03:50.457][self$download] Extract whole database of nci.cactus.
biodb.INFO [2024-06-08 16:03:50.458][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database....
biodb.DEBUG[2024-06-08 16:03:50.460][self$getDownloadPath] Download path of nci.cactus is "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/download.gz".
biodb.DEBUG[2024-06-08 16:05:05.690][private$doExtractDownload] Delete existing entry files in cache system.
biodb.DEBUG[2024-06-08 16:05:05.692][private$doExtractDownload] Extract single entries from downloaded file "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/cactus_rdfs", into "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp".
biodb.TRACE[2024-06-08 16:30:56.491][self$addFilesToCache] Moving files to cache [265242]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_1.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_2.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_3.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_4.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_5.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_6.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_7.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_8.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_9.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_10.txt, ...".
biodb.TRACE[2024-06-08 16:30:56.920][private$doAddFilesToCache] Destination files are [265242]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/1.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/2.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/3.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/4.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/5.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/6.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/7.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/8.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/9.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/10.sdf, ...".
biodb.DEBUG[2024-06-08 16:33:04.782][self$addFilesToCache] Done adding files.
biodb.DEBUG[2024-06-08 16:33:04.785][private$doExtractDownload] Delete extracted database.
biodb.TRACE[2024-06-08 16:33:04.915][self$addFilesToCache] Moving files to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/markerfd467fa4420dmarker".
biodb.TRACE[2024-06-08 16:33:04.917][private$doAddFilesToCache] Destination files are [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/extracted.marker".
biodb.DEBUG[2024-06-08 16:33:04.918][self$addFilesToCache] Done adding files.
biodb.TRACE[2024-06-08 16:33:04.920][cch$loadFileContent] Trying to load 2 files from cache: [2]: "749674, 750690".
biodb.TRACE[2024-06-08 16:33:04.922][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2024-06-08 16:33:04.934][loadFileContents] Loaded 2 files from cache: [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/749674.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/750690.sdf".
biodb.DEBUG[2024-06-08 16:33:04.936][conn$getEntryContent] 2 NCI CACTUS entry content(s) loaded from cache.
biodb.DEBUG[2024-06-08 16:33:04.938][self$createEntryFromContent] Creating NCI CACTUS entries from 2 content(s).
biodb.DEBUG[2024-06-08 16:33:04.939][self$createEntryFromContent] Parsing 2 NCI CACTUS entries.
biodb.DEBUG[2024-06-08 16:33:04.941][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-08 16:33:04.942][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:33:04.943][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:33:05.014][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:33:05.015][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:33:05.017][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:33:05.018][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-08 16:33:05.030][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:33:05.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:33:05.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:33:05.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:33:05.035][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:33:05.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:33:05.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:33:05.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:33:05.044][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-08 16:33:05.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-08 16:33:05.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:33:05.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:33:05.049][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-08 16:33:05.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-08 16:33:05.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:33:05.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:33:05.055][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-08 16:33:05.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-08 16:33:05.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:33:05.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:33:05.061][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-08 16:33:05.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-08 16:33:05.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:33:05.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:33:05.067][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-08 16:33:05.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-08 16:33:05.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:33:05.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:33:05.072][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-08 16:33:05.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-08 16:33:05.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:33:05.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:33:05.078][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-08 16:33:05.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-08 16:33:05.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:33:05.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:33:05.083][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-08 16:33:05.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-08 16:33:05.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:33:05.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:33:05.089][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:33:05.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:33:05.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:33:05.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:33:05.094][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:33:05.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:33:05.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:33:05.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:33:05.099][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:33:05.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:33:05.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:33:05.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:33:05.105][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:33:05.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:33:05.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:33:05.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:33:05.110][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:33:05.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:33:05.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:33:05.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:33:05.115][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:33:05.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:33:05.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:33:05.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:33:05.122][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:33:05.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:33:05.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:33:05.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-08 16:33:05.128][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-08 16:33:05.129][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:33:05.130][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:33:05.137][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:33:05.138][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:33:05.139][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:33:05.140][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-08 16:33:05.158][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:33:05.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:33:05.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:33:05.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:33:05.164][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:33:05.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:33:05.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:33:05.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:33:05.172][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-08 16:33:05.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-08 16:33:05.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:33:05.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:33:05.178][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-08 16:33:05.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-08 16:33:05.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:33:05.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:33:05.195][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-08 16:33:05.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-08 16:33:05.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:33:05.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:33:05.200][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-08 16:33:05.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-08 16:33:05.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:33:05.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:33:05.208][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-08 16:33:05.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-08 16:33:05.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:33:05.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:33:05.213][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-08 16:33:05.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-08 16:33:05.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:33:05.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:33:05.220][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:33:05.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:33:05.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:33:05.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:33:05.225][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:33:05.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:33:05.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:33:05.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:33:05.231][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:33:05.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:33:05.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:33:05.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:33:05.236][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:33:05.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:33:05.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:33:05.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:33:05.241][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:33:05.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:33:05.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:33:05.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:33:05.246][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:33:05.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:33:05.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:33:05.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:33:05.251][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-08 16:33:05.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-08 16:33:05.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:33:05.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:33:05.258][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-08 16:33:05.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-08 16:33:05.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:33:05.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:33:05.264][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-08 16:33:05.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-08 16:33:05.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:33:05.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:33:05.272][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-08 16:33:05.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-08 16:33:05.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:33:05.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:33:05.290][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-08 16:33:05.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-08 16:33:05.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:33:05.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:33:05.299][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:33:05.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:33:05.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:33:05.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:33:05.307][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:33:05.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:33:05.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:33:05.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:33:05.315][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:33:05.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:33:05.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:33:05.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:33:05.321][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:33:05.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-08 16:33:05.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:33:05.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:33:05.327][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:33:05.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:33:05.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:33:05.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:33:05.333][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:33:05.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:33:05.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:33:05.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:33:05.339][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:33:05.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:33:05.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:33:05.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:33:05.345][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:33:05.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:33:05.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:33:05.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:33:05.350][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:33:05.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:33:05.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:33:05.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:33:05.355][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:33:05.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:33:05.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:33:05.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:33:05.360][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:33:05.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:33:05.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:33:05.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:33:05.365][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:33:05.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:33:05.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:33:05.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:33:05.370][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-08 16:33:05.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-08 16:33:05.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:33:05.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-08 16:33:05.376][self$createEntryFromContent] Accession numbers: 749674, 750690.
biodb.TRACE[2024-06-08 16:33:05.377][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-06-08 16:33:05.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-06-08 16:33:05.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:33:05.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:33:05.382][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-06-08 16:33:05.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-06-08 16:33:05.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:33:05.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:33:05.387][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-06-08 16:33:05.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-06-08 16:33:05.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:33:05.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:33:05.398][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-06-08 16:33:05.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-06-08 16:33:05.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:33:05.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:33:05.403][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-06-08 16:33:05.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-06-08 16:33:05.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:33:05.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:33:05.408][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-06-08 16:33:05.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-06-08 16:33:05.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:33:05.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-08 16:33:05.423][biodb::testThat]
biodb.INFO [2024-06-08 16:33:05.425][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-06-08 16:33:05.426][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-08 16:33:05.427][biodb::testThat]
biodb.INFO [2024-06-08 16:33:05.435][biodb::testThat]
biodb.INFO [2024-06-08 16:33:05.437][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-06-08 16:33:05.438][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-08 16:33:05.439][biodb::testThat]
biodb.WARN [2024-06-08 16:33:05.466][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2024-06-08 16:33:05.496][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2024-06-08 16:33:05.509][biodb::testThat]
biodb.INFO [2024-06-08 16:33:05.510][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-06-08 16:33:05.511][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-08 16:33:05.513][biodb::testThat]
biodb.TRACE[2024-06-08 16:33:05.553][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-08 16:33:05.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-08 16:33:05.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:33:05.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:33:05.559][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-08 16:33:05.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-08 16:33:05.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:33:05.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:33:05.564][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-08 16:33:05.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-08 16:33:05.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:33:05.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:33:05.569][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-08 16:33:05.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-08 16:33:05.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:33:05.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:33:05.623][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-08 16:33:05.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-08 16:33:05.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:33:05.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:33:05.629][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-08 16:33:05.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-08 16:33:05.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:33:05.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:33:05.636][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-08 16:33:05.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-08 16:33:05.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:33:05.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-08 16:33:05.642][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-08 16:33:05.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-08 16:33:05.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-08 16:33:05.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-08 16:33:05.660][biodb::testThat]
biodb.INFO [2024-06-08 16:33:05.662][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-06-08 16:33:05.663][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-08 16:33:05.665][biodb::testThat]
biodb.INFO [2024-06-08 16:33:05.676][biodb::testThat]
biodb.INFO [2024-06-08 16:33:05.677][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-06-08 16:33:05.678][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-08 16:33:05.680][biodb::testThat]
biodb.INFO [2024-06-08 16:33:05.690][biodb::testThat]
biodb.INFO [2024-06-08 16:33:05.691][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-06-08 16:33:05.693][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-08 16:33:05.694][biodb::testThat]
biodb.INFO [2024-06-08 16:33:05.703][biodb::testThat]
biodb.INFO [2024-06-08 16:33:05.704][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-06-08 16:33:05.705][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-08 16:33:05.706][biodb::testThat]
biodb.INFO [2024-06-08 16:33:05.715][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-06-08 16:33:05.716][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector nci.cactus from the request scheduler
biodb.INFO [2024-06-08 16:33:05.718][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2024-06-08 16:33:05.719][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-06-08 16:33:05.720][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:33:05.721][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:33:05.722][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:33:05.723][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:33:05.725][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:33:05.726][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-06-08 16:33:05.742][biodb::testContext]
biodb.INFO [2024-06-08 16:33:05.743][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-08 16:33:05.745][biodb::testContext] Test context - Example long tests
biodb.INFO [2024-06-08 16:33:05.746][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-08 16:33:05.747][biodb::testContext]
biodb.INFO [2024-06-08 16:33:05.754][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.13.0.
biodb.DEBUG[2024-06-08 16:33:05.763][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-06-08 16:33:05.772][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-08 16:33:05.773][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-06-08 16:33:05.775][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-06-08 16:33:05.776][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:33:05.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:33:05.778][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:33:05.780][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-06-08 16:33:05.781][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-06-08 16:33:05.782][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:33:05.783][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:33:05.784][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:33:05.786][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-06-08 16:33:05.787][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-06-08 16:33:05.788][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:33:05.789][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:33:05.791][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:33:05.792][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-06-08 16:33:05.794][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-06-08 16:33:05.795][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-06-08 16:33:05.796][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:33:05.797][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:33:05.798][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:33:05.800][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-06-08 16:33:05.802][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-06-08 16:33:05.803][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-06-08 16:33:05.805][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:33:05.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:33:05.808][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:33:05.809][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-06-08 16:33:05.811][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-06-08 16:33:05.812][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:33:05.814][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:33:05.815][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:33:05.817][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-06-08 16:33:05.819][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-06-08 16:33:05.820][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-06-08 16:33:05.822][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:33:05.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:33:05.825][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:33:05.826][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-06-08 16:33:05.828][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-06-08 16:33:05.830][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:33:05.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:33:05.833][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:33:05.835][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-06-08 16:33:05.836][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-06-08 16:33:05.838][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-06-08 16:33:05.839][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:33:05.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:33:05.842][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:33:05.844][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-06-08 16:33:05.845][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-06-08 16:33:05.847][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-06-08 16:33:05.849][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-06-08 16:33:05.850][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-06-08 16:33:05.851][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-06-08 16:33:05.853][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:33:05.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:33:05.856][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:33:05.858][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-06-08 16:33:05.859][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-06-08 16:33:05.861][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:33:05.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:33:05.864][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:33:05.865][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-06-08 16:33:05.867][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-06-08 16:33:05.868][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:33:05.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:33:05.871][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:33:05.872][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-06-08 16:33:05.874][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-06-08 16:33:05.876][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:33:05.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:33:05.878][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:33:05.880][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-06-08 16:33:05.882][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-06-08 16:33:05.883][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:33:05.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:33:05.886][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:33:05.887][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-06-08 16:33:05.889][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-06-08 16:33:05.890][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:33:05.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:33:05.892][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:33:05.894][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-06-08 16:33:05.895][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-06-08 16:33:05.945][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-06-08 16:33:05.946][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:33:05.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:33:05.949][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:33:05.950][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-06-08 16:33:05.964][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-06-08 16:33:05.965][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-06-08 16:33:05.967][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:33:05.968][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:33:05.969][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[2024-06-08 16:33:05.971][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-06-08 16:33:05.973][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-08 16:33:05.974][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-06-08 16:33:05.976][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-08 16:33:05.977][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-08 16:33:05.978][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-08 16:33:05.979][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-08 16:33:05.981][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-08 16:33:05.982][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-08 16:33:05.983][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-08 16:33:05.984][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-08 16:33:05.986][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-08 16:33:05.988][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-06-08 16:33:05.989][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-08 16:33:05.991][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:33:05.992][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-08 16:33:05.993][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-08 16:33:05.993][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-08 16:33:05.993][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-08 16:33:05.993][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-08 16:33:05.993][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-08 16:33:05.995][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-08 16:33:05.996][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-08 16:33:05.997][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-08 16:33:05.998][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-08 16:33:06.000][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-08 16:33:06.001][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-08 16:33:06.002][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-08 16:33:06.003][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:33:06.004][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-08 16:33:06.006][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-08 16:33:06.007][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-08 16:33:06.008][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:33:06.010][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-06-08 16:33:06.012][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-08 16:33:06.014][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-06-08 16:33:06.015][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-08 16:33:06.016][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-08 16:33:06.018][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-08 16:33:06.019][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-08 16:33:06.021][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-08 16:33:06.022][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-08 16:33:06.023][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-08 16:33:06.024][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-08 16:33:06.026][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-08 16:33:06.027][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-06-08 16:33:06.028][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-08 16:33:06.029][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:33:06.031][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-08 16:33:06.032][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-08 16:33:06.032][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-08 16:33:06.032][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-08 16:33:06.032][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-08 16:33:06.032][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-08 16:33:06.033][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-08 16:33:06.035][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-08 16:33:06.036][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-08 16:33:06.037][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-08 16:33:06.039][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-08 16:33:06.040][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-08 16:33:06.041][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-08 16:33:06.042][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:33:06.043][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-08 16:33:06.045][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-08 16:33:06.046][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-08 16:33:06.047][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:33:06.049][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-06-08 16:33:06.051][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-08 16:33:06.052][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-06-08 16:33:06.053][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-08 16:33:06.055][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-08 16:33:06.056][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-08 16:33:06.057][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-08 16:33:06.058][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-08 16:33:06.060][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-08 16:33:06.061][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-08 16:33:06.062][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-08 16:33:06.063][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-08 16:33:06.065][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-06-08 16:33:06.066][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-08 16:33:06.067][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:33:06.068][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-08 16:33:06.070][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:33:06.071][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-08 16:33:06.072][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-08 16:33:06.073][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-08 16:33:06.074][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-08 16:33:06.076][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-08 16:33:06.077][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-08 16:33:06.078][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-08 16:33:06.079][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:33:06.080][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-08 16:33:06.082][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-08 16:33:06.083][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-08 16:33:06.084][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:33:06.085][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-06-08 16:33:06.088][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-08 16:33:06.089][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-06-08 16:33:06.090][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-08 16:33:06.092][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-08 16:33:06.094][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-08 16:33:06.095][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-08 16:33:06.096][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-08 16:33:06.097][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-08 16:33:06.098][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-08 16:33:06.100][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-08 16:33:06.101][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-08 16:33:06.102][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-06-08 16:33:06.103][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-08 16:33:06.105][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:33:06.106][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-08 16:33:06.107][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:33:06.108][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-08 16:33:06.110][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-08 16:33:06.111][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-08 16:33:06.112][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-08 16:33:06.113][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-08 16:33:06.114][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-08 16:33:06.115][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-08 16:33:06.117][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:33:06.118][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-08 16:33:06.119][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-08 16:33:06.120][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-08 16:33:06.121][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:33:06.123][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-08 16:33:06.124][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:33:06.125][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:33:06.126][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:33:06.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:33:06.129][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:33:06.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:33:06.131][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:33:06.132][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:33:06.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:33:06.134][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:33:06.135][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:33:06.136][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:33:06.138][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:33:06.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:33:06.140][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:33:06.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:33:06.142][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:33:06.143][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:33:06.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:33:06.145][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:33:06.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:33:06.147][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:33:06.149][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:33:06.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:33:06.151][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:33:06.152][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:33:06.153][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:33:06.154][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:33:06.155][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:33:06.156][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:33:06.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:33:06.159][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:33:06.160][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:33:06.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:33:06.162][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:33:06.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:33:06.164][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[2024-06-08 16:33:06.165][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:33:06.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:33:06.167][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:33:06.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:33:06.170][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:33:06.171][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:33:06.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:33:06.173][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:33:06.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:33:06.175][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:33:06.176][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:33:06.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:33:06.178][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:33:06.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:33:06.181][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:33:06.182][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:33:06.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:33:06.184][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:33:06.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:33:06.186][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:33:06.187][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:33:06.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:33:06.189][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:33:06.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:33:06.192][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:33:06.193][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:33:06.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:33:06.195][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:33:06.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:33:06.197][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:33:06.198][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:33:06.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:33:06.200][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:33:06.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:33:06.203][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:33:06.204][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:33:06.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:33:06.206][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:33:06.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:33:06.208][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:33:06.209][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:33:06.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:33:06.211][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:33:06.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:33:06.214][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:33:06.215][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:33:06.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:33:06.217][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:33:06.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:33:06.219][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:33:06.220][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-06-08 16:33:06.222][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-06-08 16:33:06.224][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-06-08 16:33:06.226][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-06-08 16:33:06.227][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-08 16:33:06.229][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-08 16:33:06.231][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-06-08 16:33:06.233][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-06-08 16:33:06.234][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-08 16:33:06.236][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-08 16:33:06.238][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-08 16:33:06.239][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-06-08 16:33:06.241][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-06-08 16:33:06.243][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-06-08 16:33:06.245][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-06-08 16:33:06.246][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-08 16:33:06.248][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-06-08 16:33:06.250][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-06-08 16:33:06.252][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-08 16:33:06.253][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-06-08 16:33:06.255][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-06-08 16:33:06.257][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-06-08 16:33:06.258][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-06-08 16:33:06.260][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-06-08 16:33:06.262][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-06-08 16:33:06.264][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-06-08 16:33:06.265][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-06-08 16:33:06.267][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-06-08 16:33:06.269][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-06-08 16:33:06.271][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-06-08 16:33:06.272][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-06-08 16:33:06.274][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-06-08 16:33:06.276][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-06-08 16:33:06.278][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-06-08 16:33:06.280][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-06-08 16:33:06.282][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-06-08 16:33:06.283][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-06-08 16:33:06.285][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-06-08 16:33:06.287][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-06-08 16:33:06.289][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-06-08 16:33:06.290][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-06-08 16:33:06.292][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-06-08 16:33:06.294][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-06-08 16:33:06.296][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-06-08 16:33:06.298][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-06-08 16:33:06.299][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-06-08 16:33:06.301][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-06-08 16:33:06.303][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-06-08 16:33:06.305][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-06-08 16:33:06.318][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-06-08 16:33:06.320][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-06-08 16:33:06.322][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-06-08 16:33:06.324][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-06-08 16:33:06.326][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-06-08 16:33:06.328][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-06-08 16:33:06.329][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-06-08 16:33:06.331][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-06-08 16:33:06.333][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-06-08 16:33:06.335][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-06-08 16:33:06.336][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-06-08 16:33:06.338][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-06-08 16:33:06.340][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-06-08 16:33:06.342][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-06-08 16:33:06.344][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-06-08 16:33:06.346][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-06-08 16:33:06.348][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-06-08 16:33:06.350][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-08 16:33:06.352][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-08 16:33:06.354][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-06-08 16:33:06.366][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-06-08 16:33:06.368][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-06-08 16:33:06.370][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-06-08 16:33:06.371][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-06-08 16:33:06.373][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-06-08 16:33:06.375][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-06-08 16:33:06.377][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-06-08 16:33:06.378][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-06-08 16:33:06.380][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-06-08 16:33:06.382][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-06-08 16:33:06.384][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-06-08 16:33:06.385][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-06-08 16:33:06.387][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-06-08 16:33:06.389][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-06-08 16:33:06.391][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-06-08 16:33:06.393][initialize] This is biodb version 1.13.0.
biodb.DEBUG[2024-06-08 16:33:06.394][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-08 16:33:06.395][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:33:06.396][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:33:06.407][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:33:06.409][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:33:06.410][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:33:06.411][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:33:06.412][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:33:06.413][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:33:06.415][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:33:06.416][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:33:06.417][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:33:06.418][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:33:06.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:33:06.420][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:33:06.421][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:33:06.423][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:33:06.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:33:06.425][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:33:06.426][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:33:06.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:33:06.429][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:33:06.430][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:33:06.431][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:33:06.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:33:06.433][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:33:06.434][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:33:06.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:33:06.436][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:33:06.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:33:06.439][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:33:06.440][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:33:06.441][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:33:06.442][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:33:06.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:33:06.444][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:33:06.445][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:33:06.446][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:33:06.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:33:06.449][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:33:06.450][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:33:06.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:33:06.452][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:33:06.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:33:06.454][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:33:06.455][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:33:06.456][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:33:06.458][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:33:06.459][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:33:06.460][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:33:06.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:33:06.462][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:33:06.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:33:06.464][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:33:06.465][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:33:06.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:33:06.468][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:33:06.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:33:06.470][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:33:06.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:33:06.472][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:33:06.473][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:33:06.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:33:06.475][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:33:06.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:33:06.478][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:33:06.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:33:06.480][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:33:06.481][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:33:06.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:33:06.483][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:33:06.484][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:33:06.485][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:33:06.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:33:06.488][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:33:06.489][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:33:06.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:33:06.491][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:33:06.492][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:33:06.493][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:33:06.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:33:06.496][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:33:06.497][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:33:06.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:33:06.499][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:33:06.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:33:06.501][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:33:06.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:33:06.503][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:33:06.504][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:33:06.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:33:06.507][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:33:06.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:33:06.509][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:33:06.510][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:33:06.511][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:33:06.512][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:33:06.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:33:06.514][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:33:06.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:33:06.517][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:33:06.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:33:06.519][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:33:06.520][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:33:06.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:33:06.522][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:33:06.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:33:06.524][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:33:06.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:33:06.527][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:33:06.528][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:33:06.529][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:33:06.530][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:33:06.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:33:06.532][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:33:06.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:33:06.535][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:33:06.536][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-08 16:33:06.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:33:06.538][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:33:06.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:33:06.541][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:33:06.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:33:06.543][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-08 16:33:06.559][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2024-06-08 16:33:06.588][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2024-06-08 16:33:06.591][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-08 16:33:06.625][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2024-06-08 16:33:06.626][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-08 16:33:06.627][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-08 16:33:06.629][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2024-06-08 16:33:06.630][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2024-06-08 16:33:06.631][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-06-08 16:33:06.632][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-08 16:33:06.634][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2024-06-08 16:33:06.635][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-08 16:33:06.636][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-08 16:33:06.637][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2024-06-08 16:33:06.639][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-08 16:33:06.640][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2024-06-08 16:33:06.640][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2024-06-08 16:33:06.640][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2024-06-08 16:33:06.640][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2024-06-08 16:33:06.640][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2024-06-08 16:33:06.640][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2024-06-08 16:33:06.640][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2024-06-08 16:33:06.641][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-06-08 16:33:06.643][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:33:06.644][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-06-08 16:33:06.645][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-08 16:33:06.646][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-08 16:33:06.647][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-08 16:33:06.649][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-08 16:33:06.650][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-08 16:33:06.651][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-08 16:33:06.652][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2024-06-08 16:33:06.652][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2024-06-08 16:33:06.652][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2024-06-08 16:33:06.652][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2024-06-08 16:33:06.654][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-08 16:33:06.655][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-08 16:33:06.656][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-06-08 16:33:06.658][self$setPropertyValue]
biodb.DEBUG[2024-06-08 16:33:06.660][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2024-06-08 16:33:06.664][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2024-06-08 16:33:06.665][super$initialize] Register connector nci.cactus with the request scheduler
biodb.DEBUG[2024-06-08 16:33:06.667][private$bdb$getRequestScheduler()$re ...] Register connector nci.cactus.
biodb.DEBUG[2024-06-08 16:33:06.669][private$addConnectorRules] Create new rule for URL "cactus.nci.nih.gov" of connector "nci.cactus".
biodb.DEBUG[2024-06-08 16:33:06.670][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-08 16:33:06.671][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-08 16:33:06.673][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-06-08 16:33:06.675][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-06-08 16:33:06.676][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-06-08 16:33:06.677][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2024-06-08 16:33:06.679][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-06-08 16:33:06.680][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector nci.cactus from the request scheduler
biodb.INFO [2024-06-08 16:33:06.681][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2024-06-08 16:33:06.682][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-06-08 16:33:06.683][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-08 16:33:06.685][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-08 16:33:06.686][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-08 16:33:06.687][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-08 16:33:06.688][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-06-08 16:33:06.689][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 92 ]
> 
> proc.time()
    user   system  elapsed 
1235.701  256.157 1763.665

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNci_1.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbNci.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.4
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘biodbNci/DESCRIPTION’ ... OK
* this is package ‘biodbNci’ version ‘1.9.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbNci’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... SKIPPED
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking 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
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c extractEntries.cpp -o extractEntries.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c test-100-example.cpp -o test-100-example.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c test-runner.cpp -o test-runner.o
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o biodbNci.so RcppExports.o extractEntries.o test-100-example.o test-runner.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.20-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)