Back to Long Tests report for BioC 3.20

This page was generated on 2025-03-01 23:55 -0500 (Sat, 01 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4768
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4503
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4526
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 1.10.0  (landing page)
Pierrick Roger
Snapshot Date: 2025-03-01 09:55 -0500 (Sat, 01 Mar 2025)
git_url: https://git.bioconductor.org/packages/biodbNci
git_branch: RELEASE_3_20
git_last_commit: d666b49
git_last_commit_date: 2024-10-29 11:09:24 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK  
palomino8Windows Server 2022 Datacenter / x64  ERROR  
merida1macOS 12.7.5 Monterey / x86_64  OK  

CHECK results for biodbNci on nebbiolo2

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: 1.10.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNci_1.10.0.tar.gz
StartedAt: 2025-03-01 16:04:26 -0500 (Sat, 01 Mar 2025)
EndedAt: 2025-03-01 16:05:25 -0500 (Sat, 01 Mar 2025)
EllapsedTime: 59.1 seconds
RetCode: 0
Status:   OK  
CheckDir: biodbNci.Rcheck
Warnings: 0

Tests output

biodbNci.Rcheck/tests/testthat.Rout


R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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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 [2025-03-01 16:05:22.220][biodb::testContext]
biodb.INFO [2025-03-01 16:05:22.222][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-01 16:05:22.223][biodb::testContext] Test context - Generic long tests
biodb.INFO [2025-03-01 16:05:22.224][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-01 16:05:22.224][biodb::testContext]
biodb.INFO [2025-03-01 16:05:22.230][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2025-03-01 16:05:22.232][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-03-01 16:05:22.238][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-01 16:05:22.239][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-01 16:05:22.240][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-01 16:05:22.241][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:22.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:22.242][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:22.243][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-01 16:05:22.259][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-01 16:05:22.260][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:22.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:22.262][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:22.263][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-01 16:05:22.264][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-01 16:05:22.264][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:22.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:22.266][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:22.267][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-01 16:05:22.268][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-01 16:05:22.269][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-01 16:05:22.269][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:22.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:22.271][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:22.272][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-01 16:05:22.273][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-01 16:05:22.274][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-01 16:05:22.274][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:22.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:22.276][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:22.277][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-01 16:05:22.278][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-01 16:05:22.278][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:22.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:22.280][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:22.281][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-01 16:05:22.282][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-01 16:05:22.283][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-01 16:05:22.283][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:22.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:22.285][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:22.286][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-01 16:05:22.287][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-01 16:05:22.287][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:22.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:22.289][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:22.290][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-01 16:05:22.291][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-01 16:05:22.292][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-01 16:05:22.292][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:22.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:22.294][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:22.295][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-01 16:05:22.296][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-01 16:05:22.297][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-01 16:05:22.297][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-01 16:05:22.298][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-01 16:05:22.299][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-01 16:05:22.300][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:22.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:22.302][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:22.302][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-01 16:05:22.303][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-01 16:05:22.304][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:22.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:22.306][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:22.307][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-01 16:05:22.308][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-01 16:05:22.308][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:22.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:22.310][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:22.311][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-01 16:05:22.312][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-01 16:05:22.312][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:22.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:22.314][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:22.315][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-01 16:05:22.316][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-01 16:05:22.317][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:22.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:22.318][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:22.319][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-01 16:05:22.320][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-01 16:05:22.321][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:22.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:22.322][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:22.323][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-01 16:05:22.324][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-01 16:05:22.328][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-01 16:05:22.329][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:22.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:22.331][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:22.332][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-01 16:05:22.333][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-01 16:05:22.334][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-01 16:05:22.334][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:22.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:22.336][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:22.339][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-01 16:05:22.369][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-01 16:05:22.389][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-03-01 16:05:22.390][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:22.391][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-01 16:05:22.391][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:22.392][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-01 16:05:22.393][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-01 16:05:22.394][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-01 16:05:22.395][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-01 16:05:22.396][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-01 16:05:22.397][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:22.398][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-01 16:05:22.398][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-01 16:05:22.399][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:05:22.400][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:22.401][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-01 16:05:22.401][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-01 16:05:22.401][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-01 16:05:22.401][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-01 16:05:22.401][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-01 16:05:22.402][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-01 16:05:22.403][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:05:22.404][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:05:22.405][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-01 16:05:22.405][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:05:22.406][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:05:22.407][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-01 16:05:22.408][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:05:22.409][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-01 16:05:22.410][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-01 16:05:22.410][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-01 16:05:22.411][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:05:22.412][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-01 16:05:22.414][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-01 16:05:22.415][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-01 16:05:22.416][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:22.417][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-01 16:05:22.417][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:22.418][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-01 16:05:22.419][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-01 16:05:22.420][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-01 16:05:22.421][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-01 16:05:22.422][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-01 16:05:22.423][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:22.424][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-01 16:05:22.425][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-01 16:05:22.425][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:05:22.426][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:22.427][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-01 16:05:22.427][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-01 16:05:22.427][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-01 16:05:22.427][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-01 16:05:22.427][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-01 16:05:22.428][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-01 16:05:22.429][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:05:22.430][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:05:22.431][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-01 16:05:22.431][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:05:22.432][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:05:22.433][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-01 16:05:22.434][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:05:22.435][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-01 16:05:22.436][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-01 16:05:22.437][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-01 16:05:22.437][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:05:22.438][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-01 16:05:22.440][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:22.441][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-03-01 16:05:22.442][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:22.443][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-01 16:05:22.444][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:22.444][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-01 16:05:22.445][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-01 16:05:22.446][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-01 16:05:22.447][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-01 16:05:22.448][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-01 16:05:22.449][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-01 16:05:22.450][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-01 16:05:22.451][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-01 16:05:22.452][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:05:22.452][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:22.453][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:05:22.454][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-01 16:05:22.455][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:05:22.456][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:05:22.457][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-01 16:05:22.458][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:05:22.458][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:05:22.459][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-01 16:05:22.460][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:05:22.461][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-01 16:05:22.462][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-01 16:05:22.463][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-01 16:05:22.463][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:05:22.464][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-01 16:05:22.466][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:22.467][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-01 16:05:22.468][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:22.469][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-01 16:05:22.470][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:22.471][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-01 16:05:22.471][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-01 16:05:22.472][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-01 16:05:22.473][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-01 16:05:22.474][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-01 16:05:22.475][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-01 16:05:22.476][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-01 16:05:22.477][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-01 16:05:22.478][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:05:22.478][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:22.479][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:05:22.480][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-01 16:05:22.481][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:05:22.482][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:05:22.483][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-01 16:05:22.484][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:05:22.484][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:05:22.485][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-01 16:05:22.486][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:05:22.487][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-01 16:05:22.488][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-01 16:05:22.489][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-01 16:05:22.490][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:05:22.493][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-01 16:05:22.494][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:22.495][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:22.495][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:22.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:22.497][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:22.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:22.499][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:22.499][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:22.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:22.501][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:22.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:22.503][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[2025-03-01 16:05:22.503][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:22.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:22.505][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:22.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:22.507][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:22.507][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:22.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:22.509][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:22.510][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:22.510][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:22.511][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:22.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:22.513][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:22.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:22.514][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:22.515][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:22.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:22.517][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:22.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:22.518][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:22.519][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:22.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:22.521][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:22.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:22.522][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:22.523][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:22.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:22.525][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:22.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:22.526][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:22.527][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:22.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:22.529][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:22.529][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:22.530][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:22.531][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:22.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:22.533][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:22.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:22.534][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:22.535][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:22.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:22.537][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:22.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:22.538][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:22.539][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:22.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:22.541][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:22.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:22.542][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:22.543][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:22.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:22.545][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:22.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:22.550][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:22.551][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:22.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:22.552][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:22.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:22.554][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:22.555][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:22.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:22.556][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:22.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:22.558][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:22.558][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:22.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:22.560][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:22.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:22.562][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:22.562][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:22.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:22.564][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:22.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:22.565][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:22.566][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-01 16:05:22.571][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-01 16:05:22.572][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-01 16:05:22.573][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-01 16:05:22.574][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-01 16:05:22.576][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-01 16:05:22.577][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-01 16:05:22.578][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-01 16:05:22.579][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-01 16:05:22.581][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-01 16:05:22.582][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-01 16:05:22.583][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-01 16:05:22.585][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-01 16:05:22.586][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-01 16:05:22.587][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-01 16:05:22.588][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-01 16:05:22.590][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-01 16:05:22.591][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-01 16:05:22.592][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-01 16:05:22.593][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-01 16:05:22.595][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-01 16:05:22.596][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-01 16:05:22.597][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-01 16:05:22.598][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-01 16:05:22.600][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-01 16:05:22.601][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-01 16:05:22.602][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-01 16:05:22.603][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-01 16:05:22.605][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-01 16:05:22.606][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-01 16:05:22.607][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-01 16:05:22.609][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-01 16:05:22.610][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-01 16:05:22.611][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-01 16:05:22.612][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-01 16:05:22.614][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-01 16:05:22.615][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-01 16:05:22.616][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-01 16:05:22.617][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-01 16:05:22.619][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-01 16:05:22.620][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-01 16:05:22.621][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-01 16:05:22.622][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-01 16:05:22.624][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-01 16:05:22.625][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-01 16:05:22.626][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-01 16:05:22.627][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-01 16:05:22.629][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-01 16:05:22.630][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-01 16:05:22.631][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-01 16:05:22.632][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-01 16:05:22.634][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-01 16:05:22.635][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-01 16:05:22.636][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-01 16:05:22.637][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-01 16:05:22.639][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-01 16:05:22.640][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-01 16:05:22.641][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-01 16:05:22.642][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-01 16:05:22.644][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-01 16:05:22.645][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-01 16:05:22.646][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-01 16:05:22.647][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-01 16:05:22.649][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-01 16:05:22.650][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-01 16:05:22.651][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-01 16:05:22.652][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-01 16:05:22.654][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-01 16:05:22.655][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-01 16:05:22.656][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-01 16:05:22.657][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-01 16:05:22.659][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-01 16:05:22.660][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-01 16:05:22.661][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-01 16:05:22.662][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-01 16:05:22.664][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-01 16:05:22.665][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-01 16:05:22.666][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-01 16:05:22.667][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-01 16:05:22.669][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-01 16:05:22.670][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-01 16:05:22.678][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-01 16:05:22.680][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-01 16:05:22.688][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-01 16:05:22.690][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2025-03-01 16:05:22.693][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-01 16:05:22.694][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:22.695][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:22.696][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:22.697][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:22.702][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:22.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:05:22.704][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:05:22.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:22.706][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:22.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:22.707][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:22.708][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:22.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:05:22.710][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:05:22.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:22.712][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:22.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:22.714][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:22.714][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:22.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:05:22.716][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:05:22.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:22.718][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:22.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:22.720][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:22.721][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:22.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:05:22.722][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:05:22.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:22.739][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:22.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:22.741][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[2025-03-01 16:05:22.742][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:22.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:05:22.743][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:05:22.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:22.745][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:22.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:22.747][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[2025-03-01 16:05:22.748][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:22.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:05:22.749][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:05:22.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:22.751][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:22.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:22.753][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:22.754][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:22.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:05:22.756][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:05:22.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:22.757][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:22.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:22.759][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:22.760][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:22.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:05:22.762][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:05:22.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:22.764][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:22.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:22.765][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:22.766][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:22.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:05:22.768][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:05:22.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:22.770][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:22.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:22.771][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:22.772][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:22.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:05:22.774][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:05:22.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:22.776][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:22.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:22.777][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:22.778][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:22.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:05:22.780][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:05:22.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:22.782][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:22.783][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:22.783][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:22.784][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:22.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:05:22.786][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:05:22.787][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:22.788][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:22.789][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:22.790][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:22.790][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:22.791][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:05:22.792][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:05:22.793][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:22.794][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:22.795][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:22.795][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:22.796][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:22.797][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:05:22.798][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:05:22.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:22.800][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:22.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:22.801][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:22.802][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:22.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:05:22.804][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:05:22.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:22.806][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:22.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:22.807][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:22.808][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:22.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:05:22.810][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:05:22.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:22.812][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:22.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:22.813][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[2025-03-01 16:05:22.814][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:22.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:05:22.816][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:05:22.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:22.818][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:22.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:22.819][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[2025-03-01 16:05:22.821][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2025-03-01 16:05:22.831][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2025-03-01 16:05:22.832][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-01 16:05:22.833][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2025-03-01 16:05:22.834][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:22.835][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-01 16:05:22.836][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-03-01 16:05:22.837][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2025-03-01 16:05:22.838][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:22.839][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-01 16:05:22.840][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2025-03-01 16:05:22.841][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-01 16:05:22.842][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:22.843][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2025-03-01 16:05:22.844][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-01 16:05:22.845][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2025-03-01 16:05:22.845][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2025-03-01 16:05:22.845][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2025-03-01 16:05:22.845][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2025-03-01 16:05:22.845][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2025-03-01 16:05:22.845][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2025-03-01 16:05:22.845][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2025-03-01 16:05:22.846][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-01 16:05:22.847][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:05:22.848][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-01 16:05:22.849][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:05:22.850][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:05:22.851][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-01 16:05:22.851][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:05:22.852][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:05:22.853][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-01 16:05:22.854][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-03-01 16:05:22.854][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-03-01 16:05:22.854][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2025-03-01 16:05:22.854][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2025-03-01 16:05:22.855][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-01 16:05:22.856][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-01 16:05:22.857][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:22.858][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:05:22.864][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2025-03-01 16:05:22.884][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2025-03-01 16:05:22.885][super$initialize] Register connector nci.cactus with the request scheduler
biodb.DEBUG[2025-03-01 16:05:22.889][private$bdb$getRequestScheduler()$re ...] Register connector nci.cactus.
biodb.DEBUG[2025-03-01 16:05:22.893][private$addConnectorRules] Create new rule for URL "cactus.nci.nih.gov" of connector "nci.cactus".
biodb.DEBUG[2025-03-01 16:05:22.897][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-01 16:05:22.898][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-01 16:05:22.899][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-03-01 16:05:22.900][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-03-01 16:05:22.901][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-03-01 16:05:22.902][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2025-03-01 16:05:22.910][biodb::testThat]
biodb.INFO [2025-03-01 16:05:22.911][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-03-01 16:05:22.912][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-01 16:05:22.913][biodb::testThat]
biodb.TRACE[2025-03-01 16:05:22.915][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.20-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-749674-content.sdf".
biodb.DEBUG[2025-03-01 16:05:22.947][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2025-03-01 16:05:22.950][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2025-03-01 16:05:22.957][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-01 16:05:22.958][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:05:22.959][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:05:22.969][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:22.970][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:22.971][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:22.972][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-01 16:05:22.988][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:22.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:22.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:22.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:22.991][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:23.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:23.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.007][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:05:23.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:05:23.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.032][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:05:23.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:05:23.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.036][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:05:23.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:05:23.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.040][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:05:23.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:05:23.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.044][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:05:23.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:05:23.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.048][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:05:23.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:05:23.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.052][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:05:23.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:05:23.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.055][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:05:23.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:05:23.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.059][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:05:23.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:05:23.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.063][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:05:23.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:05:23.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.066][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:23.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:23.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.070][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:05:23.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:05:23.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.074][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:23.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:23.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.077][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:23.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:23.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.081][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:23.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:23.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.119][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:23.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:23.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.123][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:23.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:23.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.126][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:23.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:23.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-01 16:05:23.130][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 749674.
biodb.TRACE[2025-03-01 16:05:23.132][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-01 16:05:23.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-01 16:05:23.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.136][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-01 16:05:23.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-01 16:05:23.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.139][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-01 16:05:23.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-01 16:05:23.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.143][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-01 16:05:23.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-01 16:05:23.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.159][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:23.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:23.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.173][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:05:23.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:05:23.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.180][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:23.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:23.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.184][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:23.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:23.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.187][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:23.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:23.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.192][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:23.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:23.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.196][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:23.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:23.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.199][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:23.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:23.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.203][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:05:23.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:05:23.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.207][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:05:23.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:05:23.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.210][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:05:23.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:05:23.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.224][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:23.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:23.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.227][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:23.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:23.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.231][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:23.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:23.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.234][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:23.235][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:23.236][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.237][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.238][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:23.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:23.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.248][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:05:23.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:05:23.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.251][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:05:23.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:05:23.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.255][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:05:23.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:05:23.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.258][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:05:23.259][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:05:23.260][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.261][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.262][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:05:23.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:05:23.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.272][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:05:23.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:05:23.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.275][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:05:23.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:05:23.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.279][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:05:23.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:05:23.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.282][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:05:23.283][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:05:23.284][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.285][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.286][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:05:23.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:05:23.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.295][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:05:23.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:05:23.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.299][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:05:23.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:05:23.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.302][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:05:23.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:05:23.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.306][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:05:23.307][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:05:23.308][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.309][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.309][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:05:23.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:05:23.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.319][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:05:23.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:05:23.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.323][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:05:23.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:05:23.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.326][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:05:23.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:05:23.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.330][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:05:23.331][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:05:23.331][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.332][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.333][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:05:23.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:05:23.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.343][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:23.344][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:23.344][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.345][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.349][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:05:23.354][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:05:23.354][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.355][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.359][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:05:23.360][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:05:23.361][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.361][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.365][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:05:23.366][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:05:23.367][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.368][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.371][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:05:23.372][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:05:23.373][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.374][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.389][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.20-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-750690-content.sdf".
biodb.DEBUG[2025-03-01 16:05:23.421][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2025-03-01 16:05:23.422][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2025-03-01 16:05:23.423][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-01 16:05:23.424][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:05:23.425][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:05:23.429][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:23.430][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:23.430][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:23.431][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-01 16:05:23.440][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:23.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:23.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.443][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:23.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:23.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.463][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-01 16:05:23.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-01 16:05:23.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.471][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-01 16:05:23.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-01 16:05:23.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.475][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:05:23.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:05:23.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.478][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:05:23.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:05:23.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.482][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:05:23.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:05:23.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.486][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:05:23.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:05:23.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.490][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:05:23.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:05:23.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.493][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:05:23.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:05:23.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.497][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:05:23.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:05:23.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.501][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:05:23.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:05:23.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.504][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:05:23.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:05:23.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.508][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:05:23.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:05:23.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.511][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:05:23.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:05:23.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.516][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:05:23.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:05:23.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.519][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:05:23.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:05:23.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.523][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:05:23.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:05:23.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.527][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:05:23.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:05:23.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.531][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:05:23.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:05:23.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.534][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:05:23.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:05:23.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.538][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:23.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:23.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.541][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:05:23.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:05:23.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.545][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:23.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:23.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.549][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:23.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:23.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.552][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:23.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:23.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.556][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:23.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:23.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.559][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:23.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:23.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.563][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:23.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:23.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-01 16:05:23.566][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 750690.
biodb.TRACE[2025-03-01 16:05:23.585][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-01 16:05:23.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-01 16:05:23.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.589][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-01 16:05:23.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-01 16:05:23.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.592][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-01 16:05:23.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-01 16:05:23.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.600][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-01 16:05:23.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-01 16:05:23.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.604][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:23.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:23.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.610][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:05:23.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:05:23.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.617][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:23.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:23.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.621][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:23.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:23.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.624][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:23.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:23.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.629][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:23.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:23.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.633][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:23.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:23.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.636][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:23.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:23.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.640][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:05:23.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:05:23.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.644][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:05:23.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:05:23.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.647][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:05:23.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:05:23.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.665][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:23.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:23.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.669][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:23.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:23.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.672][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:23.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:23.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.676][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:23.677][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:23.678][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.679][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.680][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:23.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:23.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.690][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-01 16:05:23.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-01 16:05:23.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.693][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-01 16:05:23.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-01 16:05:23.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.697][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-01 16:05:23.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-01 16:05:23.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.700][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-01 16:05:23.701][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-01 16:05:23.702][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.703][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.704][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-01 16:05:23.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-01 16:05:23.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.714][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:05:23.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:05:23.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.717][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:05:23.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:05:23.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.721][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:05:23.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:05:23.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.725][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:05:23.729][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:05:23.730][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.731][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.732][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:05:23.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:05:23.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.742][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:05:23.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:05:23.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.745][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:05:23.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:05:23.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.749][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:05:23.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:05:23.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.752][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:05:23.753][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:05:23.754][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.755][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.756][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:05:23.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:05:23.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.766][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:05:23.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:05:23.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.769][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:05:23.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:05:23.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.773][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:05:23.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:05:23.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.776][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:05:23.777][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:05:23.778][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.779][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.780][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:05:23.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:05:23.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.790][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:05:23.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:05:23.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.793][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:05:23.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:05:23.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.797][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:05:23.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:05:23.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.800][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:05:23.801][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:05:23.802][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.803][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.804][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:05:23.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:05:23.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.814][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:05:23.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:05:23.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.817][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:05:23.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:05:23.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.821][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:05:23.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:05:23.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.824][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:05:23.825][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:05:23.826][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.827][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.828][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:05:23.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:05:23.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.838][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:23.839][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:23.839][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.840][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.844][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-01 16:05:23.845][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-01 16:05:23.846][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.847][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.850][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:05:23.851][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:05:23.852][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.853][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.861][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:05:23.861][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:05:23.862][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.863][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.867][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:05:23.868][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:05:23.869][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.869][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.873][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:05:23.874][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:05:23.875][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.876][ef$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.880][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:05:23.881][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:05:23.882][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.882][ef$get] fields variable is a list.
biodb.INFO [2025-03-01 16:05:23.889][biodb::testThat]
biodb.INFO [2025-03-01 16:05:23.889][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-03-01 16:05:23.890][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-01 16:05:23.891][biodb::testThat]
biodb.DEBUG[2025-03-01 16:05:23.893][private$loadEntries] Creating entries from ids [2]: "749674, 750690".
biodb.DEBUG[2025-03-01 16:05:23.899][conn$getEntryContent] Get NCI CACTUS entry content(s) for 2 id(s)...
biodb.DEBUG[2025-03-01 16:05:23.904][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2025-03-01 16:05:23.905][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.TRACE[2025-03-01 16:05:23.907][cch$loadFileContent] Trying to load 2 files from cache: [2]: "749674, 750690".
biodb.TRACE[2025-03-01 16:05:23.908][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2025-03-01 16:05:23.910][loadFileContents] Loaded 2 files from cache: [2]: "/home/biocbuild/.cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/749674.sdf, /home/biocbuild/.cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/750690.sdf".
biodb.DEBUG[2025-03-01 16:05:23.911][conn$getEntryContent] 2 NCI CACTUS entry content(s) loaded from cache.
biodb.DEBUG[2025-03-01 16:05:23.912][self$createEntryFromContent] Creating NCI CACTUS entries from 2 content(s).
biodb.DEBUG[2025-03-01 16:05:23.913][self$createEntryFromContent] Parsing 2 NCI CACTUS entries.
biodb.DEBUG[2025-03-01 16:05:23.914][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-01 16:05:23.915][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:05:23.916][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:05:23.919][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:23.920][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:23.921][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:23.922][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-01 16:05:23.928][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:23.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:23.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.932][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:23.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:23.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.936][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:05:23.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:05:23.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.940][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:05:23.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:05:23.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.944][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:05:23.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:05:23.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.947][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:05:23.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:05:23.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.952][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:05:23.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:05:23.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.955][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:05:23.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:05:23.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.959][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:05:23.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:05:23.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.962][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:05:23.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:05:23.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.967][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:05:23.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:05:23.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.970][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:05:23.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:05:23.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.974][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:23.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:23.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.977][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:05:23.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:05:23.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.981][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:23.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:23.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.984][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:23.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:23.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:23.988][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:23.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:23.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:23.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-01 16:05:23.991][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-01 16:05:23.992][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:05:23.997][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:05:24.001][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:24.002][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:24.003][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:24.004][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-01 16:05:24.012][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:24.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:24.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:24.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:24.015][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:24.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:24.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:24.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:24.020][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-01 16:05:24.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-01 16:05:24.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:24.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:24.024][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-03-01 16:05:24.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-03-01 16:05:24.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:24.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:24.028][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:05:24.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:05:24.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:24.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:24.031][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-01 16:05:24.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-01 16:05:24.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:24.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:24.035][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:05:24.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:05:24.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:24.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:24.039][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-01 16:05:24.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-01 16:05:24.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:24.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:24.042][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:05:24.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:05:24.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:24.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:24.046][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:05:24.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:05:24.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:24.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:24.050][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:05:24.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:05:24.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:24.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:24.053][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:05:24.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:05:24.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:24.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:24.057][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:05:24.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:05:24.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:24.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:24.060][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:05:24.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:05:24.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:24.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:24.064][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-01 16:05:24.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-01 16:05:24.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:24.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:24.068][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:05:24.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:05:24.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:24.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:24.072][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-01 16:05:24.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-01 16:05:24.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:24.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:24.075][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:05:24.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:05:24.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:24.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:24.079][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-01 16:05:24.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-01 16:05:24.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:24.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:24.083][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:05:24.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:05:24.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:24.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:24.087][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:05:24.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:05:24.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:24.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:24.090][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:24.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:24.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:24.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:24.094][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:05:24.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-03-01 16:05:24.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:24.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:24.097][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:24.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:24.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:24.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:24.101][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:24.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:24.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:24.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:24.104][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:24.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:24.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:24.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:24.108][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:24.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:24.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:24.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:24.111][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:24.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:24.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:24.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:24.115][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:24.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:24.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:24.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:24.118][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:24.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:24.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:24.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:24.126][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:24.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:24.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:24.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:24.129][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-01 16:05:24.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-01 16:05:24.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:24.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-01 16:05:24.133][self$createEntryFromContent] Accession numbers: 749674, 750690.
biodb.TRACE[2025-03-01 16:05:24.134][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-03-01 16:05:24.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-03-01 16:05:24.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:24.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:24.137][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-03-01 16:05:24.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-03-01 16:05:24.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:24.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:24.141][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-03-01 16:05:24.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-03-01 16:05:24.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:24.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:24.148][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-03-01 16:05:24.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-03-01 16:05:24.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:24.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:24.151][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-03-01 16:05:24.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-03-01 16:05:24.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:24.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:24.155][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-03-01 16:05:24.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-03-01 16:05:24.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:24.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-01 16:05:24.164][biodb::testThat]
biodb.INFO [2025-03-01 16:05:24.165][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-03-01 16:05:24.166][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-01 16:05:24.166][biodb::testThat]
biodb.INFO [2025-03-01 16:05:24.171][biodb::testThat]
biodb.INFO [2025-03-01 16:05:24.172][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-03-01 16:05:24.173][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-01 16:05:24.174][biodb::testThat]
biodb.WARN [2025-03-01 16:05:24.192][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2025-03-01 16:05:24.209][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2025-03-01 16:05:24.216][biodb::testThat]
biodb.INFO [2025-03-01 16:05:24.217][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-03-01 16:05:24.218][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-01 16:05:24.219][biodb::testThat]
biodb.TRACE[2025-03-01 16:05:24.238][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-01 16:05:24.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-01 16:05:24.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:24.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:24.246][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-01 16:05:24.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-01 16:05:24.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:24.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:24.249][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-01 16:05:24.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-01 16:05:24.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:24.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:24.253][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-01 16:05:24.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-01 16:05:24.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:24.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:24.285][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-01 16:05:24.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-01 16:05:24.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:24.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:24.289][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-01 16:05:24.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-01 16:05:24.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:24.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:24.293][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-01 16:05:24.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-01 16:05:24.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:24.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-01 16:05:24.296][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-01 16:05:24.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-01 16:05:24.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-01 16:05:24.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-01 16:05:24.304][biodb::testThat]
biodb.INFO [2025-03-01 16:05:24.305][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-03-01 16:05:24.306][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-01 16:05:24.307][biodb::testThat]
biodb.INFO [2025-03-01 16:05:24.313][biodb::testThat]
biodb.INFO [2025-03-01 16:05:24.314][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-03-01 16:05:24.315][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-01 16:05:24.315][biodb::testThat]
biodb.INFO [2025-03-01 16:05:24.321][biodb::testThat]
biodb.INFO [2025-03-01 16:05:24.322][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-03-01 16:05:24.323][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-01 16:05:24.324][biodb::testThat]
biodb.INFO [2025-03-01 16:05:24.329][biodb::testThat]
biodb.INFO [2025-03-01 16:05:24.330][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-03-01 16:05:24.331][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-01 16:05:24.332][biodb::testThat]
biodb.INFO [2025-03-01 16:05:24.336][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-01 16:05:24.337][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector nci.cactus from the request scheduler
biodb.INFO [2025-03-01 16:05:24.338][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2025-03-01 16:05:24.339][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-01 16:05:24.340][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:05:24.341][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:05:24.341][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:24.342][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:24.343][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:24.344][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-03-01 16:05:24.352][biodb::testContext]
biodb.INFO [2025-03-01 16:05:24.353][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-01 16:05:24.354][biodb::testContext] Test context - Example long tests
biodb.INFO [2025-03-01 16:05:24.355][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-01 16:05:24.355][biodb::testContext]
biodb.INFO [2025-03-01 16:05:24.357][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2025-03-01 16:05:24.363][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-03-01 16:05:24.366][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-01 16:05:24.367][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-01 16:05:24.368][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-01 16:05:24.368][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:24.369][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:24.370][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:24.371][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-01 16:05:24.372][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-01 16:05:24.373][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:24.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:24.374][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:24.375][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-01 16:05:24.376][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-01 16:05:24.377][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:24.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:24.378][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:24.379][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-01 16:05:24.380][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-01 16:05:24.381][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-01 16:05:24.382][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:24.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:24.383][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:24.384][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-01 16:05:24.385][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-01 16:05:24.386][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-01 16:05:24.387][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:24.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:24.388][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:24.389][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-01 16:05:24.390][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-01 16:05:24.391][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:24.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:24.393][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:24.393][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-01 16:05:24.394][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-01 16:05:24.395][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-01 16:05:24.396][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:24.397][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:24.398][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:24.398][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-01 16:05:24.399][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-01 16:05:24.400][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:24.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:24.402][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:24.403][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-01 16:05:24.404][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-01 16:05:24.404][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-01 16:05:24.405][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:24.406][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:24.407][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:24.408][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-01 16:05:24.409][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-01 16:05:24.409][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-01 16:05:24.410][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-01 16:05:24.411][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-01 16:05:24.412][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-01 16:05:24.413][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:24.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:24.414][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[2025-03-01 16:05:24.415][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-01 16:05:24.416][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-01 16:05:24.417][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:24.418][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:24.419][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:24.419][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-01 16:05:24.420][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-01 16:05:24.421][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:24.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:24.423][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:24.424][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-01 16:05:24.425][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-01 16:05:24.425][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:24.426][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:24.427][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:24.428][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-01 16:05:24.429][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-01 16:05:24.429][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:24.430][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:24.431][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:24.432][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-01 16:05:24.433][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-01 16:05:24.434][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:24.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:24.435][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:24.436][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-01 16:05:24.437][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-01 16:05:24.440][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-01 16:05:24.441][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:24.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:24.442][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:24.443][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-01 16:05:24.444][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-01 16:05:24.445][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-01 16:05:24.446][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:24.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:24.447][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:24.448][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-01 16:05:24.450][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-01 16:05:24.451][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-03-01 16:05:24.452][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:24.453][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-01 16:05:24.453][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:24.454][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-01 16:05:24.455][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-01 16:05:24.456][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-01 16:05:24.457][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-01 16:05:24.458][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-01 16:05:24.459][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:24.460][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-01 16:05:24.461][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-01 16:05:24.461][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:05:24.462][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:24.463][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-01 16:05:24.463][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-01 16:05:24.463][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-01 16:05:24.463][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-01 16:05:24.463][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-01 16:05:24.464][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-01 16:05:24.465][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:05:24.466][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:05:24.467][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-01 16:05:24.467][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:05:24.468][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:05:24.469][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-01 16:05:24.470][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:05:24.471][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-01 16:05:24.472][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-01 16:05:24.472][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-01 16:05:24.473][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:05:24.474][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-01 16:05:24.476][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-01 16:05:24.477][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-01 16:05:24.478][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:24.479][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-01 16:05:24.479][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:24.480][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-01 16:05:24.481][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-01 16:05:24.482][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-01 16:05:24.487][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-01 16:05:24.488][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-01 16:05:24.488][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:24.489][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-01 16:05:24.490][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-01 16:05:24.491][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:05:24.492][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:24.493][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-01 16:05:24.493][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-01 16:05:24.493][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-01 16:05:24.493][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-01 16:05:24.493][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-01 16:05:24.494][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-01 16:05:24.495][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:05:24.495][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:05:24.496][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-01 16:05:24.497][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:05:24.498][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:05:24.499][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-01 16:05:24.500][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:05:24.500][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-01 16:05:24.501][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-01 16:05:24.502][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-01 16:05:24.503][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:05:24.504][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-01 16:05:24.506][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:24.506][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-03-01 16:05:24.507][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:24.508][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-01 16:05:24.509][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:24.510][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-01 16:05:24.511][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-01 16:05:24.512][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-01 16:05:24.513][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-01 16:05:24.513][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-01 16:05:24.514][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-01 16:05:24.515][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-01 16:05:24.516][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-01 16:05:24.517][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:05:24.518][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:24.519][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:05:24.520][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-01 16:05:24.521][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:05:24.521][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:05:24.522][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-01 16:05:24.523][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:05:24.524][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:05:24.525][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-01 16:05:24.526][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:05:24.526][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-01 16:05:24.527][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-01 16:05:24.528][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-01 16:05:24.529][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:05:24.530][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-01 16:05:24.531][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:24.532][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-01 16:05:24.533][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:24.534][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-01 16:05:24.535][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:24.536][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-01 16:05:24.537][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-01 16:05:24.538][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-01 16:05:24.539][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-01 16:05:24.539][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-01 16:05:24.540][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-01 16:05:24.541][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-01 16:05:24.542][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-01 16:05:24.543][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:05:24.544][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:24.545][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:05:24.546][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-01 16:05:24.547][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:05:24.548][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:05:24.548][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-01 16:05:24.549][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:05:24.550][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:05:24.551][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-01 16:05:24.552][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:05:24.553][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-01 16:05:24.553][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-01 16:05:24.554][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-01 16:05:24.555][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:05:24.556][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-01 16:05:24.557][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:24.558][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:24.559][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:24.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:24.560][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:24.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:24.562][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:24.563][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:24.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:24.564][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:24.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:24.566][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:24.567][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:24.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:24.568][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:24.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:24.570][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:24.571][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:24.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:24.572][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:24.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:24.574][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:24.575][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:24.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:24.576][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:24.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:24.578][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:24.579][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:24.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:24.580][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:24.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:24.582][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:24.582][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:24.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:24.584][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:24.585][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:24.586][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:24.586][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:24.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:24.588][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:24.589][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:24.590][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:24.590][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:24.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:24.592][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:24.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:24.593][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:24.594][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:24.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:24.596][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:24.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:24.597][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:24.598][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:24.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:24.600][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:24.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:24.601][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:24.602][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:24.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:24.604][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:24.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:24.609][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:24.610][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:24.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:24.611][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:24.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:24.613][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:24.614][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:24.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:24.615][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:24.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:24.617][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:24.617][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:24.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:24.619][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:24.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:24.621][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:24.621][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:24.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:24.623][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:24.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:24.625][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:24.625][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:24.626][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:24.627][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:24.628][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:24.629][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:24.629][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-01 16:05:24.631][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-01 16:05:24.632][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-01 16:05:24.633][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-01 16:05:24.635][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-01 16:05:24.636][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-01 16:05:24.637][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-01 16:05:24.638][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-01 16:05:24.639][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-01 16:05:24.641][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-01 16:05:24.642][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-01 16:05:24.643][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-01 16:05:24.644][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-01 16:05:24.646][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-01 16:05:24.647][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-01 16:05:24.648][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-01 16:05:24.649][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-01 16:05:24.651][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-01 16:05:24.652][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-01 16:05:24.653][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-01 16:05:24.654][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-01 16:05:24.656][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-01 16:05:24.657][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-01 16:05:24.658][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-01 16:05:24.659][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-01 16:05:24.661][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-01 16:05:24.662][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-01 16:05:24.663][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-01 16:05:24.664][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-01 16:05:24.666][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-01 16:05:24.667][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-01 16:05:24.668][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-01 16:05:24.669][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-01 16:05:24.671][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-01 16:05:24.672][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-01 16:05:24.673][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-01 16:05:24.674][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-01 16:05:24.675][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-01 16:05:24.677][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-01 16:05:24.678][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-01 16:05:24.679][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-01 16:05:24.680][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-01 16:05:24.682][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-01 16:05:24.683][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-01 16:05:24.684][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-01 16:05:24.685][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-01 16:05:24.687][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-01 16:05:24.688][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-01 16:05:24.689][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-01 16:05:24.690][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-01 16:05:24.692][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-01 16:05:24.693][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-01 16:05:24.694][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-01 16:05:24.695][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-01 16:05:24.697][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-01 16:05:24.698][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-01 16:05:24.699][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-01 16:05:24.700][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-01 16:05:24.702][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-01 16:05:24.703][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-01 16:05:24.704][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-01 16:05:24.705][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-01 16:05:24.706][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-01 16:05:24.708][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-01 16:05:24.709][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-01 16:05:24.710][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-01 16:05:24.711][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-01 16:05:24.713][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-01 16:05:24.714][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-01 16:05:24.715][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-01 16:05:24.716][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-01 16:05:24.718][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-01 16:05:24.719][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-01 16:05:24.720][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-01 16:05:24.721][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-01 16:05:24.723][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-01 16:05:24.728][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-01 16:05:24.729][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-01 16:05:24.730][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-01 16:05:24.732][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-01 16:05:24.733][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-01 16:05:24.734][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-01 16:05:24.736][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-01 16:05:24.737][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-01 16:05:24.738][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2025-03-01 16:05:24.739][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-01 16:05:24.740][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:24.741][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:24.742][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:24.743][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:24.744][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:24.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:05:24.745][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:05:24.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:24.747][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:24.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:24.749][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:24.749][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:24.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:05:24.751][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:05:24.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:24.753][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:24.754][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:24.754][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:24.755][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:24.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:05:24.757][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:05:24.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:24.759][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:24.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:24.760][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:24.761][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:24.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:05:24.763][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:05:24.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:24.764][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:24.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:24.766][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:24.766][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:24.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:05:24.768][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:05:24.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:24.770][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:24.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:24.771][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:24.772][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:24.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:05:24.774][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:05:24.774][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:24.775][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:24.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:24.777][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:24.777][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:24.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:05:24.779][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:05:24.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:24.781][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:24.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:24.782][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:24.783][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:24.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:05:24.785][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:05:24.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:24.786][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:24.787][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:24.788][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:24.788][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:24.789][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:05:24.790][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:05:24.791][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:24.792][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:24.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:24.793][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:24.794][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:24.795][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:05:24.796][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:05:24.796][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:24.797][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:24.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:24.799][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:24.799][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:24.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:05:24.801][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:05:24.802][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:24.803][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:24.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:24.804][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:24.805][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:24.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:05:24.807][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:05:24.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:24.808][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:24.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:24.810][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:24.811][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:24.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:05:24.812][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:05:24.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:24.814][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:24.814][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:24.815][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[2025-03-01 16:05:24.816][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:24.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:05:24.818][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:05:24.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:24.819][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:24.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:24.821][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:24.822][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:24.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:05:24.823][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:05:24.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:24.825][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:24.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:24.826][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:24.827][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:24.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:05:24.829][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:05:24.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:24.830][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:24.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:24.832][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:24.833][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-01 16:05:24.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:05:24.834][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:05:24.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:24.836][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:24.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:24.837][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-01 16:05:24.839][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2025-03-01 16:05:24.840][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2025-03-01 16:05:24.842][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-01 16:05:24.843][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2025-03-01 16:05:24.844][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:24.845][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-01 16:05:24.849][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-03-01 16:05:24.850][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2025-03-01 16:05:24.851][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:24.852][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-01 16:05:24.853][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2025-03-01 16:05:24.854][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-01 16:05:24.855][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:24.855][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2025-03-01 16:05:24.856][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-01 16:05:24.857][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2025-03-01 16:05:24.857][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2025-03-01 16:05:24.857][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2025-03-01 16:05:24.857][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2025-03-01 16:05:24.857][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2025-03-01 16:05:24.857][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2025-03-01 16:05:24.857][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2025-03-01 16:05:24.858][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-01 16:05:24.859][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:05:24.860][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-01 16:05:24.861][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:05:24.862][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:05:24.862][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-01 16:05:24.863][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-01 16:05:24.864][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-01 16:05:24.865][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-01 16:05:24.866][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-03-01 16:05:24.866][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-03-01 16:05:24.866][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2025-03-01 16:05:24.866][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2025-03-01 16:05:24.867][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-01 16:05:24.868][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-01 16:05:24.868][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-01 16:05:24.869][self$setPropertyValue]
biodb.DEBUG[2025-03-01 16:05:24.871][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2025-03-01 16:05:24.873][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2025-03-01 16:05:24.874][super$initialize] Register connector nci.cactus with the request scheduler
biodb.DEBUG[2025-03-01 16:05:24.875][private$bdb$getRequestScheduler()$re ...] Register connector nci.cactus.
biodb.DEBUG[2025-03-01 16:05:24.877][private$addConnectorRules] Create new rule for URL "cactus.nci.nih.gov" of connector "nci.cactus".
biodb.DEBUG[2025-03-01 16:05:24.878][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-01 16:05:24.879][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-01 16:05:24.880][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-03-01 16:05:24.881][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-03-01 16:05:24.882][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-03-01 16:05:24.883][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2025-03-01 16:05:24.884][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-01 16:05:24.885][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector nci.cactus from the request scheduler
biodb.INFO [2025-03-01 16:05:24.886][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2025-03-01 16:05:24.886][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-01 16:05:24.887][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-01 16:05:24.888][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-01 16:05:24.889][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-01 16:05:24.890][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-01 16:05:24.890][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-01 16:05:24.891][FUN] Functions in observer 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 
  4.077   0.178   4.246

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNci_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc-longtests/meat/biodbNci.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.2 LTS
* 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 ‘1.10.0’
* 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: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking installed package size ... NOTE
  installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
* 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 loading without being on the library search path ... 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.20-bioc-longtests/meat/biodbNci.Rcheck/00check.log’
for details.

Installation output

biodbNci.Rcheck/00install.out

* installing *source* package ‘biodbNci’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c extractEntries.cpp -o extractEntries.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c test-100-example.cpp -o test-100-example.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c test-runner.cpp -o test-runner.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o biodbNci.so RcppExports.o extractEntries.o test-100-example.o test-runner.o -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR
installing to /home/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)