Back to Long Tests report for BioC 3.19

This page was generated on 2024-05-18 23:55:02 -0400 (Sat, 18 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4751
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4485
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4515
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 12/33HostnameOS / ArchCHECK
biodbNci 1.8.0  (landing page)
Pierrick Roger
Snapshot Date: 2024-05-18 09:55:01 -0400 (Sat, 18 May 2024)
git_url: https://git.bioconductor.org/packages/biodbNci
git_branch: RELEASE_3_19
git_last_commit: 0db4525
git_last_commit_date: 2024-04-30 11:41:04 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK  
palomino3Windows Server 2022 Datacenter / x64  OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK  

CHECK results for biodbNci on lconway


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: 1.8.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNci_1.8.0.tar.gz
StartedAt: 2024-05-18 16:00:51 -0400 (Sat, 18 May 2024)
EndedAt: 2024-05-18 16:01:51 -0400 (Sat, 18 May 2024)
EllapsedTime: 60.0 seconds
RetCode: 0
Status:   OK  
CheckDir: biodbNci.Rcheck
Warnings: 0

Tests output

biodbNci.Rcheck/tests/testthat.Rout


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

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

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Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbNci)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbNci")
biodb.INFO [2024-05-18 16:01:48.784][biodb::testContext]
biodb.INFO [2024-05-18 16:01:48.787][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-18 16:01:48.788][biodb::testContext] Test context - Generic long tests
biodb.INFO [2024-05-18 16:01:48.789][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-18 16:01:48.790][biodb::testContext]
biodb.INFO [2024-05-18 16:01:48.795][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-05-18 16:01:48.797][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-05-18 16:01:48.803][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-18 16:01:48.803][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-05-18 16:01:48.804][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-05-18 16:01:48.805][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:48.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:48.806][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:48.807][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-05-18 16:01:48.821][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-05-18 16:01:48.822][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:48.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:48.824][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:48.824][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-05-18 16:01:48.825][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-05-18 16:01:48.826][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:48.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:48.827][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:48.828][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-05-18 16:01:48.829][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-05-18 16:01:48.830][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-05-18 16:01:48.830][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:48.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:48.832][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[2024-05-18 16:01:48.833][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-05-18 16:01:48.833][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-05-18 16:01:48.834][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-05-18 16:01:48.835][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:48.836][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:48.836][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:48.837][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-05-18 16:01:48.838][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-05-18 16:01:48.839][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:48.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:48.840][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:48.841][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-05-18 16:01:48.841][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-05-18 16:01:48.842][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-05-18 16:01:48.843][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:48.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:48.844][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:48.845][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-05-18 16:01:48.846][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-05-18 16:01:48.847][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:48.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:48.848][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:48.849][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-05-18 16:01:48.850][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-05-18 16:01:48.851][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-05-18 16:01:48.852][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:48.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:48.853][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:48.854][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-05-18 16:01:48.855][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-05-18 16:01:48.855][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-05-18 16:01:48.856][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-05-18 16:01:48.857][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-05-18 16:01:48.858][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-05-18 16:01:48.859][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:48.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:48.860][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:48.861][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-05-18 16:01:48.862][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-05-18 16:01:48.863][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:48.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:48.864][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:48.865][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-05-18 16:01:48.866][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-05-18 16:01:48.867][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:48.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:48.868][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:48.869][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-05-18 16:01:48.870][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-05-18 16:01:48.871][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:48.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:48.872][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:48.873][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-05-18 16:01:48.874][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-05-18 16:01:48.875][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:48.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:48.876][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:48.877][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-05-18 16:01:48.878][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-05-18 16:01:48.878][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:48.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:48.880][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:48.880][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-05-18 16:01:48.881][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-05-18 16:01:48.900][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-05-18 16:01:48.901][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:48.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:48.903][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:48.904][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-05-18 16:01:48.904][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-05-18 16:01:48.905][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-05-18 16:01:48.906][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:48.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:48.907][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:48.910][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-05-18 16:01:48.936][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-18 16:01:48.954][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-05-18 16:01:48.955][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-18 16:01:48.956][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-18 16:01:48.957][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-18 16:01:48.957][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-18 16:01:48.958][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-18 16:01:48.959][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-18 16:01:48.960][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-18 16:01:48.961][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-18 16:01:48.962][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-18 16:01:48.962][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-05-18 16:01:48.963][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-18 16:01:48.964][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:01:48.965][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-18 16:01:48.966][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-18 16:01:48.966][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-18 16:01:48.966][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-18 16:01:48.966][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-18 16:01:48.966][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-18 16:01:48.967][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-18 16:01:48.967][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-18 16:01:48.968][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-18 16:01:48.969][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-18 16:01:48.970][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-18 16:01:48.971][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-18 16:01:48.971][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-18 16:01:48.972][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:01:48.973][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-18 16:01:48.974][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-18 16:01:48.974][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-18 16:01:48.975][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:01:48.976][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-05-18 16:01:48.978][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-18 16:01:48.979][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-05-18 16:01:48.979][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-18 16:01:48.980][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-18 16:01:48.981][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-18 16:01:48.982][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-18 16:01:48.983][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-18 16:01:48.984][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-18 16:01:48.984][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-18 16:01:48.985][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-18 16:01:48.986][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-18 16:01:48.987][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-05-18 16:01:48.988][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-18 16:01:48.988][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:01:48.989][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-18 16:01:48.990][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-18 16:01:48.990][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-18 16:01:48.990][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-18 16:01:48.990][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-18 16:01:48.990][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-18 16:01:48.991][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-18 16:01:48.992][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-18 16:01:48.992][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-18 16:01:48.993][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-18 16:01:48.994][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-18 16:01:48.995][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-18 16:01:48.995][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-18 16:01:48.996][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:01:48.997][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-18 16:01:48.998][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-18 16:01:48.999][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-18 16:01:48.999][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:01:49.000][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-05-18 16:01:49.002][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-18 16:01:49.003][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-05-18 16:01:49.004][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-18 16:01:49.004][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-18 16:01:49.005][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-18 16:01:49.006][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-18 16:01:49.007][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-18 16:01:49.008][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-18 16:01:49.008][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-18 16:01:49.009][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-18 16:01:49.010][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-18 16:01:49.011][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-05-18 16:01:49.012][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-18 16:01:49.013][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:01:49.013][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-18 16:01:49.014][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:01:49.015][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-18 16:01:49.016][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-18 16:01:49.017][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-18 16:01:49.017][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-18 16:01:49.018][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-18 16:01:49.019][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-18 16:01:49.020][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-18 16:01:49.021][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:01:49.021][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-18 16:01:49.022][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-18 16:01:49.023][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-18 16:01:49.024][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:01:49.025][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-05-18 16:01:49.026][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-18 16:01:49.027][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-05-18 16:01:49.028][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-18 16:01:49.028][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-18 16:01:49.029][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-18 16:01:49.030][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-18 16:01:49.031][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-18 16:01:49.032][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-18 16:01:49.032][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-18 16:01:49.033][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-18 16:01:49.034][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-18 16:01:49.035][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-05-18 16:01:49.036][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-18 16:01:49.037][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:01:49.037][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-18 16:01:49.038][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:01:49.039][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-18 16:01:49.040][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-18 16:01:49.041][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-18 16:01:49.041][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-18 16:01:49.042][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-18 16:01:49.043][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-18 16:01:49.044][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-18 16:01:49.045][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:01:49.045][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-18 16:01:49.046][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-18 16:01:49.047][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-18 16:01:49.048][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:01:49.051][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-18 16:01:49.051][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:49.052][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:49.053][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:49.053][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:01:49.054][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:01:49.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:49.056][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:49.056][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:49.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:01:49.058][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:01:49.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:49.059][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:49.060][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:49.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:01:49.061][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:01:49.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:49.062][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:49.063][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:49.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:01:49.065][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:01:49.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:49.066][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:49.067][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:49.067][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:01:49.068][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:01:49.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:49.070][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:49.070][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:49.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:01:49.072][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:01:49.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:49.073][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:49.074][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:49.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:01:49.075][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:01:49.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:49.077][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:49.077][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:49.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:01:49.079][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:01:49.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:49.080][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:49.081][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:49.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:01:49.082][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:01:49.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:49.084][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:49.084][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:49.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:01:49.086][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:01:49.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:49.087][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:49.092][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:49.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:01:49.093][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:01:49.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:49.095][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:49.096][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:49.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:01:49.097][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:01:49.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:49.098][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:49.099][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:49.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:01:49.101][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:01:49.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:49.102][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:49.103][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:49.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:01:49.104][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:01:49.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:49.105][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:49.106][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:49.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:01:49.107][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:01:49.108][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:49.109][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:49.110][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:49.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:01:49.111][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:01:49.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:49.112][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:49.113][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:49.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:01:49.114][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:01:49.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:49.116][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:49.117][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-05-18 16:01:49.120][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-05-18 16:01:49.121][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-05-18 16:01:49.122][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-05-18 16:01:49.123][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-18 16:01:49.125][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-05-18 16:01:49.126][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-05-18 16:01:49.127][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-05-18 16:01:49.128][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-05-18 16:01:49.129][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-05-18 16:01:49.130][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-18 16:01:49.131][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-05-18 16:01:49.132][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-05-18 16:01:49.133][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-05-18 16:01:49.135][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-05-18 16:01:49.136][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-18 16:01:49.137][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-05-18 16:01:49.138][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-05-18 16:01:49.139][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-18 16:01:49.140][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-05-18 16:01:49.141][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-05-18 16:01:49.142][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-05-18 16:01:49.143][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-05-18 16:01:49.145][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-05-18 16:01:49.146][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-05-18 16:01:49.147][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-05-18 16:01:49.148][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-05-18 16:01:49.149][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-05-18 16:01:49.150][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-05-18 16:01:49.151][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-05-18 16:01:49.152][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-05-18 16:01:49.154][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-05-18 16:01:49.155][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-05-18 16:01:49.156][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-05-18 16:01:49.157][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-05-18 16:01:49.158][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-05-18 16:01:49.159][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-05-18 16:01:49.160][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-05-18 16:01:49.161][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-05-18 16:01:49.163][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-05-18 16:01:49.164][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-05-18 16:01:49.165][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-05-18 16:01:49.166][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-05-18 16:01:49.167][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-05-18 16:01:49.168][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-05-18 16:01:49.170][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-05-18 16:01:49.171][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-05-18 16:01:49.172][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-05-18 16:01:49.173][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-05-18 16:01:49.174][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-05-18 16:01:49.175][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-05-18 16:01:49.176][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-05-18 16:01:49.178][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-05-18 16:01:49.179][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-05-18 16:01:49.180][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-05-18 16:01:49.181][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-05-18 16:01:49.182][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-05-18 16:01:49.183][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-05-18 16:01:49.184][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-05-18 16:01:49.186][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-05-18 16:01:49.187][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-05-18 16:01:49.188][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-05-18 16:01:49.189][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-05-18 16:01:49.190][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-05-18 16:01:49.191][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-05-18 16:01:49.192][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-05-18 16:01:49.194][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-18 16:01:49.195][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-18 16:01:49.196][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-05-18 16:01:49.197][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-05-18 16:01:49.198][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-05-18 16:01:49.199][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-05-18 16:01:49.200][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-05-18 16:01:49.202][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-05-18 16:01:49.203][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-05-18 16:01:49.204][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-05-18 16:01:49.205][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-05-18 16:01:49.206][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-05-18 16:01:49.207][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-05-18 16:01:49.209][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-05-18 16:01:49.210][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-05-18 16:01:49.211][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-05-18 16:01:49.212][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-05-18 16:01:49.217][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-05-18 16:01:49.218][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-05-18 16:01:49.221][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-18 16:01:49.222][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:01:49.223][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:01:49.223][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:49.224][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:49.228][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:49.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:01:49.229][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:01:49.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:01:49.231][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:01:49.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:49.232][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:49.233][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:49.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:01:49.235][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:01:49.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:01:49.241][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:01:49.242][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:49.243][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:49.243][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:49.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:01:49.245][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:01:49.246][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:01:49.246][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:01:49.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:49.248][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:49.248][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:49.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:01:49.250][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:01:49.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:01:49.251][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:01:49.252][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:49.253][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:49.254][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:49.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:01:49.255][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:01:49.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:01:49.257][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:01:49.257][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:49.258][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:49.259][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:49.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:01:49.261][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:01:49.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:01:49.262][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:01:49.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:49.264][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:49.264][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:49.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:01:49.266][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:01:49.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:01:49.267][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:01:49.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:49.269][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:49.270][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:49.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:01:49.271][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:01:49.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:01:49.273][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:01:49.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:49.274][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:49.275][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:49.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:01:49.277][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:01:49.277][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:01:49.278][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:01:49.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:49.280][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[2024-05-18 16:01:49.280][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:49.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:01:49.282][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:01:49.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:01:49.283][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:01:49.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:49.285][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:49.285][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:49.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:01:49.287][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:01:49.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:01:49.288][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:01:49.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:49.290][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:49.291][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:49.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:01:49.293][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:01:49.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:01:49.295][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:01:49.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:49.297][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:49.298][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:49.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:01:49.300][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:01:49.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:01:49.301][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:01:49.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:49.304][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:49.305][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:49.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:01:49.307][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:01:49.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:01:49.309][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:01:49.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:49.311][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:49.312][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:49.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:01:49.313][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:01:49.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:01:49.315][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:01:49.316][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:49.317][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:49.318][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:49.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:01:49.319][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:01:49.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:01:49.321][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:01:49.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:49.322][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[2024-05-18 16:01:49.323][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:49.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:01:49.325][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:01:49.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:01:49.326][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:01:49.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:49.328][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:49.330][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.19-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2024-05-18 16:01:49.338][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2024-05-18 16:01:49.340][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-18 16:01:49.341][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2024-05-18 16:01:49.341][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-18 16:01:49.342][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-18 16:01:49.343][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2024-05-18 16:01:49.344][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2024-05-18 16:01:49.345][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-05-18 16:01:49.345][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-18 16:01:49.346][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2024-05-18 16:01:49.347][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-18 16:01:49.348][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-18 16:01:49.349][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2024-05-18 16:01:49.349][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-18 16:01:49.350][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2024-05-18 16:01:49.350][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2024-05-18 16:01:49.350][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2024-05-18 16:01:49.350][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2024-05-18 16:01:49.350][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2024-05-18 16:01:49.350][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2024-05-18 16:01:49.350][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2024-05-18 16:01:49.351][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-05-18 16:01:49.353][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:01:49.353][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-05-18 16:01:49.354][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-18 16:01:49.355][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-18 16:01:49.356][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-18 16:01:49.357][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-18 16:01:49.357][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-18 16:01:49.358][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-18 16:01:49.359][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2024-05-18 16:01:49.359][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2024-05-18 16:01:49.359][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2024-05-18 16:01:49.359][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2024-05-18 16:01:49.360][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-18 16:01:49.361][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-18 16:01:49.362][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-05-18 16:01:49.362][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:01:49.367][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2024-05-18 16:01:49.390][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2024-05-18 16:01:49.391][super$initialize] Register connector nci.cactus with the request scheduler
biodb.DEBUG[2024-05-18 16:01:49.394][private$bdb$getRequestScheduler()$re ...] Register connector nci.cactus.
biodb.DEBUG[2024-05-18 16:01:49.398][private$addConnectorRules] Create new rule for URL "cactus.nci.nih.gov" of connector "nci.cactus".
biodb.DEBUG[2024-05-18 16:01:49.401][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-18 16:01:49.402][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-18 16:01:49.403][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-05-18 16:01:49.404][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-05-18 16:01:49.405][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-05-18 16:01:49.406][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2024-05-18 16:01:49.442][biodb::testThat]
biodb.INFO [2024-05-18 16:01:49.443][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-05-18 16:01:49.444][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-18 16:01:49.445][biodb::testThat]
biodb.TRACE[2024-05-18 16:01:49.448][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.19-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-749674-content.sdf".
biodb.DEBUG[2024-05-18 16:01:49.449][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2024-05-18 16:01:49.452][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2024-05-18 16:01:49.459][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-18 16:01:49.460][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:01:49.461][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:01:49.473][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:01:49.474][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:01:49.474][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:49.475][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-18 16:01:49.490][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:01:49.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:01:49.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:49.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:49.493][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:01:49.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:01:49.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:49.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:49.507][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-18 16:01:49.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-18 16:01:49.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:49.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:49.529][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-18 16:01:49.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-18 16:01:49.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:49.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:49.533][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-18 16:01:49.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-18 16:01:49.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:49.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:49.537][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-18 16:01:49.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-18 16:01:49.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:49.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:49.541][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-18 16:01:49.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-18 16:01:49.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:49.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:49.544][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-18 16:01:49.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-18 16:01:49.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:49.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:49.548][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-18 16:01:49.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-18 16:01:49.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:49.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:49.551][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-18 16:01:49.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-18 16:01:49.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:49.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:49.555][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-05-18 16:01:49.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-05-18 16:01:49.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:49.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:49.558][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-05-18 16:01:49.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-05-18 16:01:49.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:49.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:49.561][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:01:49.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:01:49.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:49.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:49.564][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-05-18 16:01:49.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-05-18 16:01:49.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:49.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:49.568][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:01:49.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:01:49.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:49.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:49.571][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:01:49.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:01:49.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:49.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:49.574][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:01:49.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:01:49.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:49.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:49.609][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:01:49.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:01:49.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:49.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:49.612][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:01:49.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:01:49.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:49.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:49.615][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:01:49.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:01:49.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:49.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-18 16:01:49.619][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 749674.
biodb.TRACE[2024-05-18 16:01:49.621][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-18 16:01:49.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-18 16:01:49.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:49.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:49.624][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-18 16:01:49.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-18 16:01:49.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:49.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:49.627][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-18 16:01:49.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-18 16:01:49.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:49.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:49.630][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-18 16:01:49.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-18 16:01:49.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:49.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:49.646][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:01:49.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:01:49.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:49.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:49.660][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-05-18 16:01:49.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-05-18 16:01:49.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:49.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:49.668][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:01:49.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:01:49.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:49.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:49.671][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:01:49.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:01:49.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:49.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:49.675][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:01:49.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:01:49.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:49.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:49.680][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:01:49.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:01:49.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:49.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:49.683][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:01:49.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:01:49.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:49.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:49.687][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:01:49.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:01:49.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:49.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:49.690][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-05-18 16:01:49.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-05-18 16:01:49.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:49.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:49.694][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-05-18 16:01:49.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-05-18 16:01:49.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:49.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:49.697][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-05-18 16:01:49.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-05-18 16:01:49.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:49.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:49.712][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:01:49.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:01:49.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:49.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:49.715][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:01:49.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:01:49.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:49.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:49.719][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:01:49.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:01:49.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:49.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:49.722][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:01:49.723][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:01:49.724][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:49.724][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:49.725][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:01:49.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:01:49.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:49.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:49.737][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-18 16:01:49.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-18 16:01:49.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:49.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:49.740][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-18 16:01:49.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-18 16:01:49.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:49.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:49.743][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-18 16:01:49.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-18 16:01:49.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:49.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:49.747][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-18 16:01:49.748][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-18 16:01:49.748][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:49.749][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:49.750][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-18 16:01:49.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-18 16:01:49.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:49.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:49.760][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-18 16:01:49.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-18 16:01:49.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:49.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:49.763][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-18 16:01:49.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-18 16:01:49.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:49.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:49.767][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-18 16:01:49.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-18 16:01:49.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:49.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:49.770][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-18 16:01:49.771][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-18 16:01:49.772][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:49.773][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:49.774][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-18 16:01:49.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-18 16:01:49.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:49.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:49.784][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-18 16:01:49.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-18 16:01:49.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:49.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:49.788][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-18 16:01:49.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-18 16:01:49.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:49.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:49.791][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-18 16:01:49.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-18 16:01:49.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:49.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:49.795][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-18 16:01:49.795][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-18 16:01:49.796][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:49.797][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:49.798][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-18 16:01:49.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-18 16:01:49.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:49.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:49.809][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-18 16:01:49.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-18 16:01:49.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:49.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:49.812][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-18 16:01:49.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-18 16:01:49.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:49.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:49.816][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-18 16:01:49.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-18 16:01:49.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:49.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:49.819][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-18 16:01:49.820][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-18 16:01:49.821][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:49.822][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:49.822][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-18 16:01:49.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-18 16:01:49.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:49.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:49.833][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:01:49.834][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:01:49.835][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:49.836][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:49.845][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-18 16:01:49.846][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-18 16:01:49.846][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:49.847][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:49.852][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-18 16:01:49.853][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-18 16:01:49.854][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:49.854][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:49.859][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-18 16:01:49.860][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-18 16:01:49.861][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:49.862][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:49.866][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-18 16:01:49.867][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-18 16:01:49.868][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:49.869][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:49.884][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.19-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-750690-content.sdf".
biodb.DEBUG[2024-05-18 16:01:49.911][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2024-05-18 16:01:49.913][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2024-05-18 16:01:49.914][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-18 16:01:49.915][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:01:49.915][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:01:49.920][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:01:49.921][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:01:49.922][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:49.923][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-18 16:01:49.930][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:01:49.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:01:49.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:49.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:49.934][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:01:49.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:01:49.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:49.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:49.951][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-05-18 16:01:49.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-05-18 16:01:49.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:49.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:49.959][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-05-18 16:01:49.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-05-18 16:01:49.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:49.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:49.963][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-18 16:01:49.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-18 16:01:49.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:49.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:49.966][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-18 16:01:49.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-18 16:01:49.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:49.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:49.970][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-18 16:01:49.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-18 16:01:49.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:49.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:49.973][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-18 16:01:49.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-18 16:01:49.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:49.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:49.977][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:01:49.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:01:49.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:49.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:49.980][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:01:49.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:01:49.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:49.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:49.984][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:01:49.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:01:49.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:49.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:49.988][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:01:49.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:01:49.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:49.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:49.993][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:01:49.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:01:49.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:49.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:49.998][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:01:49.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:01:50.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.003][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:01:50.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:01:50.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.010][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-18 16:01:50.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-18 16:01:50.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.015][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-18 16:01:50.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-18 16:01:50.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.019][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-18 16:01:50.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-18 16:01:50.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.023][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-18 16:01:50.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-18 16:01:50.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.027][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-05-18 16:01:50.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-05-18 16:01:50.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.030][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-05-18 16:01:50.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-05-18 16:01:50.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.034][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:01:50.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:01:50.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.037][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-05-18 16:01:50.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-05-18 16:01:50.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.040][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:01:50.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:01:50.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.043][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:01:50.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:01:50.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.047][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:01:50.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:01:50.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.051][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:01:50.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:01:50.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.054][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:01:50.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:01:50.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.059][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:01:50.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:01:50.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-18 16:01:50.064][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 750690.
biodb.TRACE[2024-05-18 16:01:50.085][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-18 16:01:50.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-18 16:01:50.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.089][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-18 16:01:50.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-18 16:01:50.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.092][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-18 16:01:50.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-18 16:01:50.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.099][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-18 16:01:50.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-18 16:01:50.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.104][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:01:50.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:01:50.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.111][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-05-18 16:01:50.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-05-18 16:01:50.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.119][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:01:50.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:01:50.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.123][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:01:50.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:01:50.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.126][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:01:50.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:01:50.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.131][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:01:50.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:01:50.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.135][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:01:50.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:01:50.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.139][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:01:50.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:01:50.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.145][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-05-18 16:01:50.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-05-18 16:01:50.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.148][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-05-18 16:01:50.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-05-18 16:01:50.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.152][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-05-18 16:01:50.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-05-18 16:01:50.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.170][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:01:50.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:01:50.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.174][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:01:50.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:01:50.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.177][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:01:50.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:01:50.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.180][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:01:50.181][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:01:50.182][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.183][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.184][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:01:50.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:01:50.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.194][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-05-18 16:01:50.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-05-18 16:01:50.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.198][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-05-18 16:01:50.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-05-18 16:01:50.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.201][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-05-18 16:01:50.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-05-18 16:01:50.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.204][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-05-18 16:01:50.205][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-05-18 16:01:50.206][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.207][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.208][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-05-18 16:01:50.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-05-18 16:01:50.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.219][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:01:50.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:01:50.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.222][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:01:50.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:01:50.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.226][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:01:50.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:01:50.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.229][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:01:50.230][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:01:50.231][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.231][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.237][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:01:50.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:01:50.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.247][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-18 16:01:50.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-18 16:01:50.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.251][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-18 16:01:50.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-18 16:01:50.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.254][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-18 16:01:50.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-18 16:01:50.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.259][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-18 16:01:50.260][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-18 16:01:50.261][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.262][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.263][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-18 16:01:50.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-18 16:01:50.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.276][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-18 16:01:50.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-18 16:01:50.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.279][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-18 16:01:50.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-18 16:01:50.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.283][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-18 16:01:50.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-18 16:01:50.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.286][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-18 16:01:50.287][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-18 16:01:50.288][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.288][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.289][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-18 16:01:50.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-18 16:01:50.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.300][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-18 16:01:50.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-18 16:01:50.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.304][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-18 16:01:50.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-18 16:01:50.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.307][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-18 16:01:50.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-18 16:01:50.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.310][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-18 16:01:50.311][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-18 16:01:50.312][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.313][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.314][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-18 16:01:50.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-18 16:01:50.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.326][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-18 16:01:50.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-18 16:01:50.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.329][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-18 16:01:50.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-18 16:01:50.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.333][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-18 16:01:50.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-18 16:01:50.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.336][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-18 16:01:50.337][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-18 16:01:50.338][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.339][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.340][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-18 16:01:50.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-18 16:01:50.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.351][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:01:50.352][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:01:50.353][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.353][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.358][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-05-18 16:01:50.359][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-05-18 16:01:50.360][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.361][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.365][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-18 16:01:50.366][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-18 16:01:50.367][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.368][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.372][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-18 16:01:50.373][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-18 16:01:50.374][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.379][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.384][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-18 16:01:50.385][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-18 16:01:50.386][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.386][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.391][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-18 16:01:50.392][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-18 16:01:50.393][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.393][ef$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.398][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:01:50.399][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:01:50.400][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.401][ef$get] fields variable is a list.
biodb.INFO [2024-05-18 16:01:50.408][biodb::testThat]
biodb.INFO [2024-05-18 16:01:50.409][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-05-18 16:01:50.410][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-18 16:01:50.411][biodb::testThat]
biodb.DEBUG[2024-05-18 16:01:50.412][private$loadEntries] Creating entries from ids [2]: "749674, 750690".
biodb.DEBUG[2024-05-18 16:01:50.418][conn$getEntryContent] Get NCI CACTUS entry content(s) for 2 id(s)...
biodb.DEBUG[2024-05-18 16:01:50.421][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2024-05-18 16:01:50.422][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.TRACE[2024-05-18 16:01:50.424][cch$loadFileContent] Trying to load 2 files from cache: [2]: "749674, 750690".
biodb.TRACE[2024-05-18 16:01:50.425][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2024-05-18 16:01:50.427][loadFileContents] Loaded 2 files from cache: [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/749674.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/750690.sdf".
biodb.DEBUG[2024-05-18 16:01:50.428][conn$getEntryContent] 2 NCI CACTUS entry content(s) loaded from cache.
biodb.DEBUG[2024-05-18 16:01:50.429][self$createEntryFromContent] Creating NCI CACTUS entries from 2 content(s).
biodb.DEBUG[2024-05-18 16:01:50.430][self$createEntryFromContent] Parsing 2 NCI CACTUS entries.
biodb.DEBUG[2024-05-18 16:01:50.431][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-18 16:01:50.432][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:01:50.433][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:01:50.437][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:01:50.438][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:01:50.438][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:50.439][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-18 16:01:50.445][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:01:50.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:01:50.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.448][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:01:50.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:01:50.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.452][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-18 16:01:50.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-18 16:01:50.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.455][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-18 16:01:50.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-18 16:01:50.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.459][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-18 16:01:50.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-18 16:01:50.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.462][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-18 16:01:50.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-18 16:01:50.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.466][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-18 16:01:50.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-18 16:01:50.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.470][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-18 16:01:50.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-18 16:01:50.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.473][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-18 16:01:50.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-18 16:01:50.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.476][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-18 16:01:50.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-18 16:01:50.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.480][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-05-18 16:01:50.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-05-18 16:01:50.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.483][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-05-18 16:01:50.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-05-18 16:01:50.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.486][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:01:50.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:01:50.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.490][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-05-18 16:01:50.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-05-18 16:01:50.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.493][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:01:50.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:01:50.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.496][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:01:50.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:01:50.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.499][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:01:50.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:01:50.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-18 16:01:50.503][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-18 16:01:50.503][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:01:50.504][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:01:50.509][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:01:50.510][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:01:50.515][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:50.515][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-18 16:01:50.522][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:01:50.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:01:50.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.525][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:01:50.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:01:50.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.529][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-05-18 16:01:50.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-05-18 16:01:50.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.532][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-05-18 16:01:50.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-05-18 16:01:50.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.536][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-18 16:01:50.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-18 16:01:50.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.539][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-18 16:01:50.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-18 16:01:50.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.542][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-18 16:01:50.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-18 16:01:50.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.546][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-18 16:01:50.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-18 16:01:50.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.549][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:01:50.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:01:50.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.552][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:01:50.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:01:50.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.556][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:01:50.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:01:50.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.559][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:01:50.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:01:50.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.562][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:01:50.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:01:50.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.565][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:01:50.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:01:50.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.569][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-18 16:01:50.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-18 16:01:50.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.573][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-18 16:01:50.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-18 16:01:50.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.576][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-18 16:01:50.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-18 16:01:50.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.579][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-18 16:01:50.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-18 16:01:50.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.583][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-18 16:01:50.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-18 16:01:50.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.586][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-05-18 16:01:50.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-05-18 16:01:50.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.589][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-05-18 16:01:50.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-05-18 16:01:50.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.592][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:01:50.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:01:50.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.595][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-05-18 16:01:50.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-05-18 16:01:50.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.599][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:01:50.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:01:50.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.602][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:01:50.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:01:50.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.605][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:01:50.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:01:50.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.609][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:01:50.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:01:50.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.612][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:01:50.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:01:50.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.615][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:01:50.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:01:50.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.618][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:01:50.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:01:50.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.622][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:01:50.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:01:50.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.625][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-18 16:01:50.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-18 16:01:50.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-18 16:01:50.632][self$createEntryFromContent] Accession numbers: 749674, 750690.
biodb.TRACE[2024-05-18 16:01:50.633][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-05-18 16:01:50.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-05-18 16:01:50.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.636][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-05-18 16:01:50.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-05-18 16:01:50.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.639][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-05-18 16:01:50.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-05-18 16:01:50.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.646][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-05-18 16:01:50.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-05-18 16:01:50.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.650][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-05-18 16:01:50.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-05-18 16:01:50.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.653][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-05-18 16:01:50.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-05-18 16:01:50.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-18 16:01:50.664][biodb::testThat]
biodb.INFO [2024-05-18 16:01:50.664][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-05-18 16:01:50.665][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-18 16:01:50.666][biodb::testThat]
biodb.INFO [2024-05-18 16:01:50.672][biodb::testThat]
biodb.INFO [2024-05-18 16:01:50.672][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-05-18 16:01:50.673][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-18 16:01:50.674][biodb::testThat]
biodb.WARN [2024-05-18 16:01:50.690][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2024-05-18 16:01:50.705][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2024-05-18 16:01:50.714][biodb::testThat]
biodb.INFO [2024-05-18 16:01:50.715][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-05-18 16:01:50.715][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-18 16:01:50.716][biodb::testThat]
biodb.TRACE[2024-05-18 16:01:50.736][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-18 16:01:50.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-18 16:01:50.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.739][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-18 16:01:50.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-18 16:01:50.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.742][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-18 16:01:50.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-18 16:01:50.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.751][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-18 16:01:50.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-18 16:01:50.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.788][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-18 16:01:50.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-18 16:01:50.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.792][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-18 16:01:50.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-18 16:01:50.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.796][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-18 16:01:50.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-18 16:01:50.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-18 16:01:50.800][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-18 16:01:50.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-18 16:01:50.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-18 16:01:50.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-18 16:01:50.809][biodb::testThat]
biodb.INFO [2024-05-18 16:01:50.810][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-05-18 16:01:50.811][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-18 16:01:50.812][biodb::testThat]
biodb.INFO [2024-05-18 16:01:50.821][biodb::testThat]
biodb.INFO [2024-05-18 16:01:50.822][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-05-18 16:01:50.823][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-18 16:01:50.824][biodb::testThat]
biodb.INFO [2024-05-18 16:01:50.832][biodb::testThat]
biodb.INFO [2024-05-18 16:01:50.833][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-05-18 16:01:50.834][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-18 16:01:50.835][biodb::testThat]
biodb.INFO [2024-05-18 16:01:50.844][biodb::testThat]
biodb.INFO [2024-05-18 16:01:50.845][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-05-18 16:01:50.846][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-18 16:01:50.847][biodb::testThat]
biodb.INFO [2024-05-18 16:01:50.856][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-05-18 16:01:50.858][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector nci.cactus from the request scheduler
biodb.INFO [2024-05-18 16:01:50.859][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2024-05-18 16:01:50.860][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-05-18 16:01:50.861][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:01:50.862][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:01:50.863][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:01:50.864][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:01:50.865][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:50.866][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-05-18 16:01:50.875][biodb::testContext]
biodb.INFO [2024-05-18 16:01:50.876][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-18 16:01:50.877][biodb::testContext] Test context - Example long tests
biodb.INFO [2024-05-18 16:01:50.877][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-18 16:01:50.878][biodb::testContext]
biodb.INFO [2024-05-18 16:01:50.880][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-05-18 16:01:50.881][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-05-18 16:01:50.885][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-18 16:01:50.886][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-05-18 16:01:50.887][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-05-18 16:01:50.888][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:50.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:50.889][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:50.890][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-05-18 16:01:50.891][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-05-18 16:01:50.896][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:50.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:50.898][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:50.899][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-05-18 16:01:50.899][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-05-18 16:01:50.900][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:50.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:50.902][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:50.903][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-05-18 16:01:50.904][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-05-18 16:01:50.906][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-05-18 16:01:50.907][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:50.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:50.908][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:50.909][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-05-18 16:01:50.910][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-05-18 16:01:50.911][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-05-18 16:01:50.912][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:50.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:50.913][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:50.914][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-05-18 16:01:50.915][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-05-18 16:01:50.916][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:50.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:50.917][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:50.918][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-05-18 16:01:50.919][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-05-18 16:01:50.920][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-05-18 16:01:50.920][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:50.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:50.922][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:50.922][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-05-18 16:01:50.923][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-05-18 16:01:50.924][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:50.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:50.925][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:50.926][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-05-18 16:01:50.927][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-05-18 16:01:50.927][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-05-18 16:01:50.928][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:50.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:50.929][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:50.930][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-05-18 16:01:50.931][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-05-18 16:01:50.932][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-05-18 16:01:50.932][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-05-18 16:01:50.933][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-05-18 16:01:50.934][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-05-18 16:01:50.935][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:50.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:50.936][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:50.937][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-05-18 16:01:50.938][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-05-18 16:01:50.938][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:50.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:50.940][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:50.941][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-05-18 16:01:50.941][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-05-18 16:01:50.942][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:50.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:50.943][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:50.944][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-05-18 16:01:50.945][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-05-18 16:01:50.946][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:50.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:50.947][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:50.948][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-05-18 16:01:50.948][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-05-18 16:01:50.949][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:50.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:50.951][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:50.951][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-05-18 16:01:50.952][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-05-18 16:01:50.953][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:50.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:50.954][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:50.955][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-05-18 16:01:50.956][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-05-18 16:01:50.974][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-05-18 16:01:50.975][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:50.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:50.977][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:50.977][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-05-18 16:01:50.978][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-05-18 16:01:50.979][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-05-18 16:01:50.979][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:50.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:50.981][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:50.982][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-05-18 16:01:50.983][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-18 16:01:50.984][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-05-18 16:01:50.985][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-18 16:01:50.986][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-18 16:01:50.987][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-18 16:01:50.987][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-18 16:01:50.988][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-18 16:01:50.989][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-18 16:01:50.990][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-18 16:01:50.990][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-18 16:01:50.991][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-18 16:01:50.992][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-05-18 16:01:50.993][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-18 16:01:50.993][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:01:50.994][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-18 16:01:50.995][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-18 16:01:50.995][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-18 16:01:50.995][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-18 16:01:50.995][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-18 16:01:50.995][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-18 16:01:50.996][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-18 16:01:50.997][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-18 16:01:50.997][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-18 16:01:50.998][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-18 16:01:50.999][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-18 16:01:50.999][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-18 16:01:51.000][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-18 16:01:51.001][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:01:51.002][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-18 16:01:51.002][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-18 16:01:51.003][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-18 16:01:51.004][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:01:51.005][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-05-18 16:01:51.006][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-18 16:01:51.007][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-05-18 16:01:51.008][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-18 16:01:51.009][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-18 16:01:51.009][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-18 16:01:51.010][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-18 16:01:51.011][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-18 16:01:51.012][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-18 16:01:51.012][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-18 16:01:51.013][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-18 16:01:51.014][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-18 16:01:51.015][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-05-18 16:01:51.016][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-18 16:01:51.016][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:01:51.017][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-18 16:01:51.018][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-18 16:01:51.018][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-18 16:01:51.018][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-18 16:01:51.018][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-18 16:01:51.018][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-18 16:01:51.019][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-18 16:01:51.019][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-18 16:01:51.020][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-18 16:01:51.021][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-18 16:01:51.026][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-18 16:01:51.027][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-18 16:01:51.027][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-18 16:01:51.028][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:01:51.029][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-18 16:01:51.030][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-18 16:01:51.030][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-18 16:01:51.031][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:01:51.032][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-05-18 16:01:51.034][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-18 16:01:51.034][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-05-18 16:01:51.035][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-18 16:01:51.036][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-18 16:01:51.037][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-18 16:01:51.037][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-18 16:01:51.038][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-18 16:01:51.039][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-18 16:01:51.040][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-18 16:01:51.040][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-18 16:01:51.041][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-18 16:01:51.042][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-05-18 16:01:51.043][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-18 16:01:51.043][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:01:51.044][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-18 16:01:51.045][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:01:51.046][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-18 16:01:51.047][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-18 16:01:51.047][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-18 16:01:51.048][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-18 16:01:51.049][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-18 16:01:51.049][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-18 16:01:51.050][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-18 16:01:51.051][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:01:51.051][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-18 16:01:51.052][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-18 16:01:51.053][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-18 16:01:51.053][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:01:51.054][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-05-18 16:01:51.056][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-18 16:01:51.057][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-05-18 16:01:51.057][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-18 16:01:51.058][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-18 16:01:51.059][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-18 16:01:51.059][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-18 16:01:51.060][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-18 16:01:51.061][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-18 16:01:51.062][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-18 16:01:51.062][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-18 16:01:51.063][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-18 16:01:51.064][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-05-18 16:01:51.065][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-18 16:01:51.065][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:01:51.066][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-18 16:01:51.067][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:01:51.068][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-18 16:01:51.068][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-18 16:01:51.069][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-18 16:01:51.070][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-18 16:01:51.070][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-18 16:01:51.071][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-18 16:01:51.072][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-18 16:01:51.072][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:01:51.073][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-18 16:01:51.074][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-18 16:01:51.074][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-18 16:01:51.075][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:01:51.076][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-18 16:01:51.077][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:51.078][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:51.078][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:51.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:01:51.080][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:01:51.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:51.081][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:51.082][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:51.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:01:51.083][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:01:51.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:51.085][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:51.085][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:51.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:01:51.087][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:01:51.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:51.088][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:51.089][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:51.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:01:51.090][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:01:51.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:51.091][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:51.092][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:51.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:01:51.094][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:01:51.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:51.095][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:51.096][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:51.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:01:51.097][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:01:51.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:51.099][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:51.099][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:51.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:01:51.101][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:01:51.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:51.102][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:51.103][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:51.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:01:51.104][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:01:51.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:51.106][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:51.106][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:51.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:01:51.108][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:01:51.108][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:51.109][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:51.110][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:51.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:01:51.111][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:01:51.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:51.113][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:51.113][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:51.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:01:51.115][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:01:51.116][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:51.116][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:51.117][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:51.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:01:51.118][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:01:51.119][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:51.120][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:51.120][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:51.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:01:51.122][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:01:51.122][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:51.123][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:51.124][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:51.125][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:01:51.125][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:01:51.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:51.127][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:51.127][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:51.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:01:51.128][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:01:51.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:51.134][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:51.134][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:51.135][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:01:51.136][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:01:51.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:51.137][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:51.137][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:51.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:01:51.139][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:01:51.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:51.140][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:51.141][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-05-18 16:01:51.142][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-05-18 16:01:51.143][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-05-18 16:01:51.144][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-05-18 16:01:51.145][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-18 16:01:51.146][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-05-18 16:01:51.147][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-05-18 16:01:51.148][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-05-18 16:01:51.149][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-05-18 16:01:51.150][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-05-18 16:01:51.151][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-18 16:01:51.152][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-05-18 16:01:51.154][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-05-18 16:01:51.155][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-05-18 16:01:51.156][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-05-18 16:01:51.157][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-18 16:01:51.158][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-05-18 16:01:51.159][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-05-18 16:01:51.160][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-18 16:01:51.161][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-05-18 16:01:51.162][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-05-18 16:01:51.163][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-05-18 16:01:51.164][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-05-18 16:01:51.165][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-05-18 16:01:51.166][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-05-18 16:01:51.167][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-05-18 16:01:51.168][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-05-18 16:01:51.169][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-05-18 16:01:51.170][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-05-18 16:01:51.172][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-05-18 16:01:51.173][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-05-18 16:01:51.174][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-05-18 16:01:51.175][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-05-18 16:01:51.176][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-05-18 16:01:51.177][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-05-18 16:01:51.178][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-05-18 16:01:51.179][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-05-18 16:01:51.180][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-05-18 16:01:51.181][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-05-18 16:01:51.182][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-05-18 16:01:51.183][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-05-18 16:01:51.184][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-05-18 16:01:51.185][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-05-18 16:01:51.186][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-05-18 16:01:51.187][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-05-18 16:01:51.188][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-05-18 16:01:51.190][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-05-18 16:01:51.191][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-05-18 16:01:51.192][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-05-18 16:01:51.193][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-05-18 16:01:51.194][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-05-18 16:01:51.195][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-05-18 16:01:51.196][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-05-18 16:01:51.197][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-05-18 16:01:51.198][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-05-18 16:01:51.199][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-05-18 16:01:51.200][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-05-18 16:01:51.201][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-05-18 16:01:51.202][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-05-18 16:01:51.203][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-05-18 16:01:51.205][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-05-18 16:01:51.206][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-05-18 16:01:51.207][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-05-18 16:01:51.208][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-05-18 16:01:51.209][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-05-18 16:01:51.210][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-05-18 16:01:51.211][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-18 16:01:51.212][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-18 16:01:51.213][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-05-18 16:01:51.214][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-05-18 16:01:51.215][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-05-18 16:01:51.216][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-05-18 16:01:51.217][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-05-18 16:01:51.218][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-05-18 16:01:51.219][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-05-18 16:01:51.220][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-05-18 16:01:51.222][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-05-18 16:01:51.223][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-05-18 16:01:51.224][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-05-18 16:01:51.225][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-05-18 16:01:51.226][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-05-18 16:01:51.227][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-05-18 16:01:51.228][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-05-18 16:01:51.229][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-05-18 16:01:51.230][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-05-18 16:01:51.231][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-18 16:01:51.232][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:01:51.237][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:01:51.238][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:51.238][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:51.239][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:51.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:01:51.241][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:01:51.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:01:51.242][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:01:51.242][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:51.243][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:51.244][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:51.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:01:51.245][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:01:51.246][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:01:51.246][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:01:51.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:51.248][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:51.249][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:51.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:01:51.250][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:01:51.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:01:51.251][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:01:51.252][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:51.253][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:51.254][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:51.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:01:51.255][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:01:51.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:01:51.256][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:01:51.257][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:51.258][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:51.258][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:51.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:01:51.260][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:01:51.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:01:51.261][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:01:51.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:51.263][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:51.263][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:51.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:01:51.265][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:01:51.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:01:51.266][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:01:51.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:51.268][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:51.268][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:51.269][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:01:51.270][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:01:51.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:01:51.271][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:01:51.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:51.273][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:51.273][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:51.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:01:51.275][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:01:51.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:01:51.276][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:01:51.277][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:51.278][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:51.278][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:51.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:01:51.280][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:01:51.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:01:51.281][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:01:51.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:51.283][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:51.284][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:51.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:01:51.285][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:01:51.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:01:51.286][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:01:51.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:51.288][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:51.289][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:51.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:01:51.290][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:01:51.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:01:51.291][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:01:51.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:51.293][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:51.293][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:51.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:01:51.295][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:01:51.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:01:51.296][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:01:51.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:51.298][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:51.298][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:51.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:01:51.300][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:01:51.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:01:51.301][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:01:51.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:51.302][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[2024-05-18 16:01:51.303][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:51.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:01:51.305][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:01:51.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:01:51.306][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:01:51.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:51.307][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:51.308][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:51.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:01:51.309][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:01:51.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:01:51.310][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:01:51.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:51.312][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:51.312][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:51.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:01:51.314][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:01:51.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:01:51.315][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:01:51.316][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:51.316][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:51.317][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-18 16:01:51.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:01:51.318][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:01:51.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:01:51.320][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:01:51.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:51.321][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-18 16:01:51.323][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.19-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2024-05-18 16:01:51.324][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2024-05-18 16:01:51.326][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-18 16:01:51.326][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2024-05-18 16:01:51.327][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-18 16:01:51.328][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-18 16:01:51.329][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2024-05-18 16:01:51.329][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2024-05-18 16:01:51.330][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-05-18 16:01:51.331][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-18 16:01:51.332][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2024-05-18 16:01:51.332][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-18 16:01:51.333][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-18 16:01:51.334][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2024-05-18 16:01:51.335][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-18 16:01:51.335][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2024-05-18 16:01:51.335][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2024-05-18 16:01:51.335][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2024-05-18 16:01:51.335][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2024-05-18 16:01:51.335][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2024-05-18 16:01:51.335][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2024-05-18 16:01:51.335][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2024-05-18 16:01:51.336][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-05-18 16:01:51.337][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:01:51.337][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-05-18 16:01:51.338][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-18 16:01:51.339][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-18 16:01:51.340][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-18 16:01:51.344][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-18 16:01:51.345][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-18 16:01:51.346][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-18 16:01:51.346][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2024-05-18 16:01:51.346][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2024-05-18 16:01:51.346][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2024-05-18 16:01:51.346][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2024-05-18 16:01:51.347][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-18 16:01:51.348][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-18 16:01:51.349][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-05-18 16:01:51.349][self$setPropertyValue]
biodb.DEBUG[2024-05-18 16:01:51.350][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2024-05-18 16:01:51.353][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2024-05-18 16:01:51.353][super$initialize] Register connector nci.cactus with the request scheduler
biodb.DEBUG[2024-05-18 16:01:51.354][private$bdb$getRequestScheduler()$re ...] Register connector nci.cactus.
biodb.DEBUG[2024-05-18 16:01:51.355][private$addConnectorRules] Create new rule for URL "cactus.nci.nih.gov" of connector "nci.cactus".
biodb.DEBUG[2024-05-18 16:01:51.356][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-18 16:01:51.357][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-18 16:01:51.358][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-05-18 16:01:51.359][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-05-18 16:01:51.360][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-05-18 16:01:51.360][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2024-05-18 16:01:51.361][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-05-18 16:01:51.362][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector nci.cactus from the request scheduler
biodb.INFO [2024-05-18 16:01:51.363][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2024-05-18 16:01:51.363][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-05-18 16:01:51.364][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-18 16:01:51.365][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-18 16:01:51.365][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-18 16:01:51.366][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-18 16:01:51.367][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-05-18 16:01:51.367][FUN] Functions in observer 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 
  3.836   0.272   4.139

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNci_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc-longtests/meat/biodbNci.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘biodbNci/DESCRIPTION’ ... OK
* this is package ‘biodbNci’ version ‘1.8.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbNci’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... SKIPPED
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
  Running ‘testthat.R’
 OK
* DONE

Status: OK

Installation output

biodbNci.Rcheck/00install.out

* installing *source* package ‘biodbNci’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c extractEntries.cpp -o extractEntries.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c test-100-example.cpp -o test-100-example.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c test-runner.cpp -o test-runner.o
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o biodbNci.so RcppExports.o extractEntries.o test-100-example.o test-runner.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.19-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)