Back to Long Tests report for BioC 3.19

This page was generated on 2024-05-11 23:55:02 -0400 (Sat, 11 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: 2024-05-11 09:55:01 -0400 (Sat, 11 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  ERROR  
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: 2024-05-11 16:00:54 -0400 (Sat, 11 May 2024)
EndedAt: 2024-05-11 16:01:57 -0400 (Sat, 11 May 2024)
EllapsedTime: 63.0 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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Type 'q()' to quit R.

> # 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 [2024-05-11 16:01:54.617][biodb::testContext]
biodb.INFO [2024-05-11 16:01:54.620][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-11 16:01:54.621][biodb::testContext] Test context - Generic long tests
biodb.INFO [2024-05-11 16:01:54.622][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-11 16:01:54.623][biodb::testContext]
biodb.INFO [2024-05-11 16:01:54.628][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-05-11 16:01:54.630][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-05-11 16:01:54.635][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-11 16:01:54.636][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-05-11 16:01:54.637][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-05-11 16:01:54.638][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:54.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:54.639][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:54.640][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-05-11 16:01:54.654][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-05-11 16:01:54.655][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:54.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:54.656][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:54.657][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-05-11 16:01:54.658][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-05-11 16:01:54.658][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:54.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:54.660][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:54.661][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-05-11 16:01:54.662][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-05-11 16:01:54.663][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-05-11 16:01:54.663][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:54.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:54.665][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:54.666][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-05-11 16:01:54.666][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-05-11 16:01:54.667][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-05-11 16:01:54.668][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:54.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:54.669][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:54.670][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-05-11 16:01:54.671][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-05-11 16:01:54.671][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:54.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:54.672][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:54.673][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-05-11 16:01:54.674][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-05-11 16:01:54.675][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-05-11 16:01:54.675][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:54.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:54.676][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:54.677][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-05-11 16:01:54.678][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-05-11 16:01:54.679][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:54.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:54.680][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:54.681][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-05-11 16:01:54.681][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-05-11 16:01:54.682][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-05-11 16:01:54.683][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:54.683][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:54.684][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:54.685][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-05-11 16:01:54.686][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-05-11 16:01:54.686][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-05-11 16:01:54.687][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-05-11 16:01:54.688][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-05-11 16:01:54.689][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-05-11 16:01:54.690][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:54.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:54.691][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:54.692][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-05-11 16:01:54.693][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-05-11 16:01:54.693][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:54.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:54.695][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:54.695][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-05-11 16:01:54.696][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-05-11 16:01:54.697][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:54.697][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:54.698][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:54.699][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-05-11 16:01:54.700][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-05-11 16:01:54.700][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:54.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:54.702][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:54.702][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-05-11 16:01:54.704][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-05-11 16:01:54.704][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:54.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:54.706][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:54.706][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-05-11 16:01:54.707][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-05-11 16:01:54.708][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:54.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:54.709][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:54.710][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-05-11 16:01:54.711][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-05-11 16:01:54.728][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-05-11 16:01:54.729][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:54.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:54.730][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:54.731][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-05-11 16:01:54.732][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-05-11 16:01:54.733][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-05-11 16:01:54.733][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:54.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:54.735][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:54.738][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-05-11 16:01:54.764][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-11 16:01:54.781][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-05-11 16:01:54.782][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-11 16:01:54.783][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-11 16:01:54.784][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-11 16:01:54.784][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-11 16:01:54.785][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-11 16:01:54.786][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-11 16:01:54.787][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-11 16:01:54.787][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-11 16:01:54.788][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-11 16:01:54.789][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-05-11 16:01:54.790][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-11 16:01:54.791][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:01:54.791][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-11 16:01:54.792][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-11 16:01:54.792][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-11 16:01:54.792][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-11 16:01:54.792][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-11 16:01:54.792][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-11 16:01:54.793][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-11 16:01:54.794][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-11 16:01:54.795][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-11 16:01:54.795][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-11 16:01:54.796][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-11 16:01:54.797][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-11 16:01:54.798][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-11 16:01:54.798][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:01:54.799][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-11 16:01:54.800][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-11 16:01:54.801][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-11 16:01:54.801][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:01:54.802][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-05-11 16:01:54.804][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-11 16:01:54.804][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-05-11 16:01:54.805][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-11 16:01:54.806][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-11 16:01:54.807][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-11 16:01:54.808][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-11 16:01:54.808][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-11 16:01:54.809][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-11 16:01:54.810][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-11 16:01:54.811][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-11 16:01:54.812][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-11 16:01:54.812][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-05-11 16:01:54.813][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-11 16:01:54.814][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:01:54.815][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-11 16:01:54.816][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-11 16:01:54.816][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-11 16:01:54.816][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-11 16:01:54.816][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-11 16:01:54.816][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-11 16:01:54.816][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-11 16:01:54.817][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-11 16:01:54.818][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-11 16:01:54.819][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-11 16:01:54.819][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-11 16:01:54.820][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-11 16:01:54.821][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-11 16:01:54.822][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:01:54.822][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-11 16:01:54.823][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-11 16:01:54.824][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-11 16:01:54.825][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:01:54.826][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-05-11 16:01:54.827][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-11 16:01:54.828][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-05-11 16:01:54.829][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-11 16:01:54.829][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-11 16:01:54.830][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-11 16:01:54.831][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-11 16:01:54.832][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-11 16:01:54.833][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-11 16:01:54.833][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-11 16:01:54.834][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-11 16:01:54.835][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-11 16:01:54.836][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-05-11 16:01:54.837][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-11 16:01:54.837][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:01:54.838][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-11 16:01:54.839][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:01:54.840][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-11 16:01:54.841][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-11 16:01:54.841][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-11 16:01:54.842][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-11 16:01:54.843][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-11 16:01:54.844][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-11 16:01:54.844][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-11 16:01:54.845][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:01:54.846][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-11 16:01:54.847][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-11 16:01:54.848][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-11 16:01:54.848][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:01:54.849][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-05-11 16:01:54.850][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-11 16:01:54.851][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-05-11 16:01:54.852][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-11 16:01:54.853][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-11 16:01:54.854][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-11 16:01:54.855][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-11 16:01:54.856][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-11 16:01:54.856][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-11 16:01:54.857][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-11 16:01:54.858][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-11 16:01:54.859][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-11 16:01:54.860][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-05-11 16:01:54.860][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-11 16:01:54.861][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:01:54.862][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-11 16:01:54.863][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:01:54.864][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-11 16:01:54.864][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-11 16:01:54.865][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-11 16:01:54.866][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-11 16:01:54.867][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-11 16:01:54.868][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-11 16:01:54.868][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-11 16:01:54.869][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:01:54.870][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-11 16:01:54.871][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-11 16:01:54.871][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-11 16:01:54.872][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:01:54.875][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-11 16:01:54.876][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:54.877][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:54.878][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:54.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:54.879][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:54.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:54.880][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[2024-05-11 16:01:54.881][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:54.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:54.882][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:54.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:54.884][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:54.884][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:54.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:54.886][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:54.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:54.887][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:54.888][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:54.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:54.889][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:54.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:54.891][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:54.891][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:54.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:54.893][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:54.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:54.894][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:54.895][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:54.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:54.896][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:54.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:54.897][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:54.898][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:54.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:54.899][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:54.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:54.901][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:54.901][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:54.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:54.903][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:54.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:54.904][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:54.905][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:54.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:54.906][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:54.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:54.908][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[2024-05-11 16:01:54.909][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:54.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:54.910][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:54.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:54.912][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:54.912][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:54.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:54.918][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:54.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:54.919][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:54.920][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:54.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:54.921][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:54.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:54.923][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:54.923][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:54.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:54.924][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:54.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:54.926][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:54.926][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:54.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:54.928][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:54.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:54.929][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[2024-05-11 16:01:54.930][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:54.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:54.931][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:54.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:54.933][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:54.933][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:54.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:54.935][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:54.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:54.936][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[2024-05-11 16:01:54.937][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:54.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:54.939][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:54.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:54.940][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[2024-05-11 16:01:54.941][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-05-11 16:01:54.945][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-05-11 16:01:54.946][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-05-11 16:01:54.947][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-05-11 16:01:54.948][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-11 16:01:54.949][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-05-11 16:01:54.951][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-05-11 16:01:54.952][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-05-11 16:01:54.953][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-05-11 16:01:54.954][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-05-11 16:01:54.955][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-11 16:01:54.956][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-05-11 16:01:54.957][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-05-11 16:01:54.958][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-05-11 16:01:54.959][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-05-11 16:01:54.960][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-11 16:01:54.961][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-05-11 16:01:54.963][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-05-11 16:01:54.964][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-11 16:01:54.965][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-05-11 16:01:54.966][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-05-11 16:01:54.967][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-05-11 16:01:54.968][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-05-11 16:01:54.969][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-05-11 16:01:54.971][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-05-11 16:01:54.972][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-05-11 16:01:54.973][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-05-11 16:01:54.974][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-05-11 16:01:54.975][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-05-11 16:01:54.976][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-05-11 16:01:54.977][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-05-11 16:01:54.978][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-05-11 16:01:54.980][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-05-11 16:01:54.981][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-05-11 16:01:54.982][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-05-11 16:01:54.983][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-05-11 16:01:54.984][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-05-11 16:01:54.985][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-05-11 16:01:54.986][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-05-11 16:01:54.987][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-05-11 16:01:54.988][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-05-11 16:01:54.990][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-05-11 16:01:54.991][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-05-11 16:01:54.992][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-05-11 16:01:54.993][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-05-11 16:01:54.994][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-05-11 16:01:54.995][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-05-11 16:01:54.996][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-05-11 16:01:54.997][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-05-11 16:01:54.998][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-05-11 16:01:54.999][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-05-11 16:01:55.000][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-05-11 16:01:55.001][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-05-11 16:01:55.003][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-05-11 16:01:55.004][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-05-11 16:01:55.005][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-05-11 16:01:55.006][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-05-11 16:01:55.007][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-05-11 16:01:55.008][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-05-11 16:01:55.009][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-05-11 16:01:55.011][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-05-11 16:01:55.012][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-05-11 16:01:55.013][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-05-11 16:01:55.014][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-05-11 16:01:55.015][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-05-11 16:01:55.016][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-05-11 16:01:55.017][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-11 16:01:55.018][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-11 16:01:55.019][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-05-11 16:01:55.020][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-05-11 16:01:55.022][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-05-11 16:01:55.023][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-05-11 16:01:55.024][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-05-11 16:01:55.025][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-05-11 16:01:55.026][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-05-11 16:01:55.027][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-05-11 16:01:55.028][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-05-11 16:01:55.029][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-05-11 16:01:55.030][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-05-11 16:01:55.031][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-05-11 16:01:55.032][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-05-11 16:01:55.033][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-05-11 16:01:55.034][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-05-11 16:01:55.038][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-05-11 16:01:55.040][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-05-11 16:01:55.042][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-11 16:01:55.043][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:55.044][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:55.044][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:55.045][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:55.049][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:55.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:01:55.050][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:01:55.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:55.052][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:55.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:55.053][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:55.054][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:55.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:01:55.055][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:01:55.056][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:55.057][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:55.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:55.063][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:55.064][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:55.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:01:55.065][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:01:55.066][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:55.067][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:55.067][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:55.068][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:55.069][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:55.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:01:55.070][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:01:55.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:55.072][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:55.072][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:55.073][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[2024-05-11 16:01:55.074][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:55.074][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:01:55.075][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:01:55.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:55.076][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:55.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:55.078][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[2024-05-11 16:01:55.079][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:55.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:01:55.080][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:01:55.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:55.081][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:55.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:55.083][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:55.084][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:55.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:01:55.085][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:01:55.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:55.086][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:55.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:55.088][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[2024-05-11 16:01:55.089][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:55.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:01:55.090][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:01:55.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:55.092][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:55.092][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:55.093][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:55.094][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:55.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:01:55.095][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:01:55.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:55.097][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:55.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:55.098][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[2024-05-11 16:01:55.099][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:55.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:01:55.100][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:01:55.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:55.102][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:55.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:55.103][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:55.104][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:55.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:01:55.105][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:01:55.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:55.107][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:55.108][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:55.108][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:55.109][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:55.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:01:55.111][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:01:55.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:55.112][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:55.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:55.114][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:55.114][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:55.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:01:55.116][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:01:55.117][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:55.117][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:55.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:55.119][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:55.119][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:55.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:01:55.121][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:01:55.122][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:55.122][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:55.123][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:55.124][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:55.125][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:55.125][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:01:55.126][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:01:55.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:55.127][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:55.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:55.129][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:55.130][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:55.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:01:55.131][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:01:55.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:55.132][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:55.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:55.134][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[2024-05-11 16:01:55.135][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:55.135][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:01:55.136][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:01:55.137][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:55.138][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:55.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:55.139][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:55.141][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.19-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2024-05-11 16:01:55.149][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2024-05-11 16:01:55.150][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-11 16:01:55.151][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2024-05-11 16:01:55.152][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-11 16:01:55.153][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-11 16:01:55.154][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2024-05-11 16:01:55.155][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2024-05-11 16:01:55.155][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-05-11 16:01:55.156][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-11 16:01:55.157][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2024-05-11 16:01:55.158][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-11 16:01:55.159][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-11 16:01:55.159][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2024-05-11 16:01:55.160][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-11 16:01:55.161][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2024-05-11 16:01:55.161][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2024-05-11 16:01:55.161][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2024-05-11 16:01:55.161][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2024-05-11 16:01:55.161][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2024-05-11 16:01:55.161][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2024-05-11 16:01:55.161][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2024-05-11 16:01:55.162][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-05-11 16:01:55.163][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:01:55.164][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-05-11 16:01:55.164][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-11 16:01:55.165][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-11 16:01:55.166][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-11 16:01:55.167][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-11 16:01:55.168][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-11 16:01:55.168][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-11 16:01:55.169][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2024-05-11 16:01:55.169][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2024-05-11 16:01:55.169][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2024-05-11 16:01:55.169][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2024-05-11 16:01:55.170][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-11 16:01:55.170][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-11 16:01:55.171][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-05-11 16:01:55.172][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:01:55.177][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2024-05-11 16:01:55.196][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2024-05-11 16:01:55.197][super$initialize] Register connector nci.cactus with the request scheduler
biodb.DEBUG[2024-05-11 16:01:55.200][private$bdb$getRequestScheduler()$re ...] Register connector nci.cactus.
biodb.DEBUG[2024-05-11 16:01:55.203][private$addConnectorRules] Create new rule for URL "cactus.nci.nih.gov" of connector "nci.cactus".
biodb.DEBUG[2024-05-11 16:01:55.206][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-11 16:01:55.207][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-11 16:01:55.208][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-05-11 16:01:55.209][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-05-11 16:01:55.210][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-05-11 16:01:55.211][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2024-05-11 16:01:55.246][biodb::testThat]
biodb.INFO [2024-05-11 16:01:55.247][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-05-11 16:01:55.248][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-11 16:01:55.248][biodb::testThat]
biodb.TRACE[2024-05-11 16:01:55.251][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[2024-05-11 16:01:55.252][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2024-05-11 16:01:55.255][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2024-05-11 16:01:55.261][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-11 16:01:55.262][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:01:55.263][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:01:55.274][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:55.275][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:55.276][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:55.276][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-11 16:01:55.291][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:55.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:55.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.294][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:55.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:55.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.308][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-11 16:01:55.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-11 16:01:55.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.328][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-11 16:01:55.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-11 16:01:55.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.332][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-11 16:01:55.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-11 16:01:55.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.335][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-11 16:01:55.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-11 16:01:55.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.339][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-11 16:01:55.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-11 16:01:55.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.343][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-11 16:01:55.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-11 16:01:55.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.346][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-11 16:01:55.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-11 16:01:55.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.349][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-11 16:01:55.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-11 16:01:55.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.353][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-05-11 16:01:55.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-05-11 16:01:55.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.356][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-05-11 16:01:55.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-05-11 16:01:55.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.360][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:55.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:55.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.363][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-05-11 16:01:55.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-05-11 16:01:55.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.366][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:55.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:55.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.369][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:55.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:55.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.372][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:55.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:55.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.406][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:55.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:55.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.410][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:55.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:55.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.413][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:55.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:55.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-11 16:01:55.416][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 749674.
biodb.TRACE[2024-05-11 16:01:55.419][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-11 16:01:55.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-11 16:01:55.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.422][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-11 16:01:55.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-11 16:01:55.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.425][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-11 16:01:55.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-11 16:01:55.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.428][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-11 16:01:55.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-11 16:01:55.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.444][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:55.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:55.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.457][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-05-11 16:01:55.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-05-11 16:01:55.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.466][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:55.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:55.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.469][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:55.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:55.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.472][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:55.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:55.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.476][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:55.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:55.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.479][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:55.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:55.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.482][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:55.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:55.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.485][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-05-11 16:01:55.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-05-11 16:01:55.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.488][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-05-11 16:01:55.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-05-11 16:01:55.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.491][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-05-11 16:01:55.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-05-11 16:01:55.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.505][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:55.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:55.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.508][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:55.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:55.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.512][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:55.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:55.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.515][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:55.516][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:55.516][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.517][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.518][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:55.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:55.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.528][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-11 16:01:55.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-11 16:01:55.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.531][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-11 16:01:55.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-11 16:01:55.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.535][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-11 16:01:55.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-11 16:01:55.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.538][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-11 16:01:55.539][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-11 16:01:55.539][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.540][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.541][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-11 16:01:55.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-11 16:01:55.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.551][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-11 16:01:55.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-11 16:01:55.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.554][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-11 16:01:55.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-11 16:01:55.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.558][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-11 16:01:55.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-11 16:01:55.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.561][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-11 16:01:55.561][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-11 16:01:55.562][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.563][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.564][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-11 16:01:55.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-11 16:01:55.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.574][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-11 16:01:55.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-11 16:01:55.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.577][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-11 16:01:55.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-11 16:01:55.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.581][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-11 16:01:55.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-11 16:01:55.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.584][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-11 16:01:55.585][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-11 16:01:55.586][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.587][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.587][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-11 16:01:55.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-11 16:01:55.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.598][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-11 16:01:55.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-11 16:01:55.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.601][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-11 16:01:55.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-11 16:01:55.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.604][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-11 16:01:55.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-11 16:01:55.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.607][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-11 16:01:55.608][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-11 16:01:55.609][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.610][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.610][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-11 16:01:55.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-11 16:01:55.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.620][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:55.621][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:55.622][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.623][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.631][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-11 16:01:55.632][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-11 16:01:55.632][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.633][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.637][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-11 16:01:55.638][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-11 16:01:55.639][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.640][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.644][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-11 16:01:55.644][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-11 16:01:55.645][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.646][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.650][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-11 16:01:55.651][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-11 16:01:55.652][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.653][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.667][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[2024-05-11 16:01:55.692][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2024-05-11 16:01:55.693][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2024-05-11 16:01:55.694][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-11 16:01:55.695][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:01:55.696][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:01:55.700][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:55.701][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:55.702][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:55.702][FUN] Functions in observer BiodbConfig: [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[2024-05-11 16:01:55.709][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:55.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:55.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.713][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:55.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:55.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.730][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-05-11 16:01:55.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-05-11 16:01:55.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.733][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-05-11 16:01:55.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-05-11 16:01:55.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.741][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-11 16:01:55.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-11 16:01:55.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.744][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-11 16:01:55.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-11 16:01:55.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.747][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-11 16:01:55.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-11 16:01:55.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.750][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-11 16:01:55.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-11 16:01:55.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.754][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:01:55.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:01:55.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.757][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:01:55.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:01:55.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.761][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:01:55.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:01:55.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.764][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:01:55.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:01:55.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.767][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:01:55.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:01:55.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.770][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:01:55.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:01:55.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.773][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:01:55.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:01:55.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.777][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-11 16:01:55.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-11 16:01:55.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.781][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-11 16:01:55.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-11 16:01:55.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.784][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-11 16:01:55.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-11 16:01:55.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.788][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-11 16:01:55.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-11 16:01:55.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.792][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-05-11 16:01:55.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-05-11 16:01:55.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.795][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-05-11 16:01:55.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-05-11 16:01:55.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.798][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:55.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:55.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.801][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-05-11 16:01:55.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-05-11 16:01:55.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.804][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:55.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:55.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.807][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:55.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:55.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.810][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:55.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:55.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.813][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:55.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:55.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.816][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:55.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:55.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.819][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:55.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:55.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-11 16:01:55.822][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 750690.
biodb.TRACE[2024-05-11 16:01:55.838][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-11 16:01:55.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-11 16:01:55.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.841][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-11 16:01:55.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-11 16:01:55.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.844][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-11 16:01:55.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-11 16:01:55.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.847][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-11 16:01:55.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-11 16:01:55.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.855][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:55.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:55.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.862][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-05-11 16:01:55.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-05-11 16:01:55.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.869][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:55.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:55.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.873][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:55.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:55.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.876][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:55.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:55.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.880][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:55.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:55.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.883][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:55.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:55.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.886][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:55.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:55.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.890][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-05-11 16:01:55.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-05-11 16:01:55.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.893][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-05-11 16:01:55.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-05-11 16:01:55.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.896][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-05-11 16:01:55.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-05-11 16:01:55.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.913][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:55.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:55.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.916][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:55.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:55.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.920][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:55.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:55.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.923][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:55.924][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:55.925][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.925][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.926][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:55.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:55.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.937][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-05-11 16:01:55.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-05-11 16:01:55.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.940][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-05-11 16:01:55.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-05-11 16:01:55.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.944][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-05-11 16:01:55.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-05-11 16:01:55.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.947][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-05-11 16:01:55.948][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-05-11 16:01:55.949][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.949][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.950][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-05-11 16:01:55.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-05-11 16:01:55.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.961][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:01:55.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:01:55.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.965][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:01:55.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:01:55.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.968][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:01:55.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:01:55.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.971][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:01:55.972][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:01:55.973][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.973][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.974][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:01:55.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:01:55.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.989][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-11 16:01:55.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-11 16:01:55.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.992][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-11 16:01:55.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-11 16:01:55.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.995][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-11 16:01:55.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-11 16:01:55.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:55.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:55.998][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-11 16:01:55.999][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-11 16:01:56.000][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:56.001][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:56.002][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-11 16:01:56.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-11 16:01:56.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:56.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:56.012][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-11 16:01:56.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-11 16:01:56.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:56.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:56.016][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-11 16:01:56.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-11 16:01:56.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:56.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:56.019][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-11 16:01:56.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-11 16:01:56.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:56.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:56.022][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-11 16:01:56.023][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-11 16:01:56.024][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:56.025][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:56.025][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-11 16:01:56.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-11 16:01:56.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:56.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:56.036][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-11 16:01:56.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-11 16:01:56.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:56.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:56.039][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-11 16:01:56.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-11 16:01:56.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:56.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:56.042][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-11 16:01:56.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-11 16:01:56.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:56.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:56.046][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-11 16:01:56.047][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-11 16:01:56.047][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:56.048][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:56.049][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-11 16:01:56.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-11 16:01:56.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:56.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:56.059][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-11 16:01:56.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-11 16:01:56.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:56.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:56.063][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-11 16:01:56.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-11 16:01:56.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:56.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:56.066][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-11 16:01:56.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-11 16:01:56.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:56.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:56.069][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-11 16:01:56.070][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-11 16:01:56.070][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:56.071][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:56.072][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-11 16:01:56.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-11 16:01:56.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:56.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:56.083][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:56.084][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:56.084][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:56.085][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:56.090][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-05-11 16:01:56.091][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-05-11 16:01:56.092][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:56.092][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:56.097][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-11 16:01:56.098][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-11 16:01:56.099][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:56.099][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:56.104][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-11 16:01:56.105][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-11 16:01:56.105][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:56.106][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:56.115][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-11 16:01:56.116][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-11 16:01:56.117][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:56.118][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:56.122][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-11 16:01:56.123][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-11 16:01:56.124][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:56.124][ef$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:56.129][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:01:56.130][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:01:56.131][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:56.131][ef$get] fields variable is a list.
biodb.INFO [2024-05-11 16:01:56.139][biodb::testThat]
biodb.INFO [2024-05-11 16:01:56.140][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-05-11 16:01:56.140][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-11 16:01:56.141][biodb::testThat]
biodb.DEBUG[2024-05-11 16:01:56.143][private$loadEntries] Creating entries from ids [2]: "749674, 750690".
biodb.DEBUG[2024-05-11 16:01:56.148][conn$getEntryContent] Get NCI CACTUS entry content(s) for 2 id(s)...
biodb.DEBUG[2024-05-11 16:01:56.153][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2024-05-11 16:01:56.154][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.TRACE[2024-05-11 16:01:56.156][cch$loadFileContent] Trying to load 2 files from cache: [2]: "749674, 750690".
biodb.TRACE[2024-05-11 16:01:56.157][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2024-05-11 16:01:56.172][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[2024-05-11 16:01:56.173][conn$getEntryContent] 2 NCI CACTUS entry content(s) loaded from cache.
biodb.DEBUG[2024-05-11 16:01:56.174][self$createEntryFromContent] Creating NCI CACTUS entries from 2 content(s).
biodb.DEBUG[2024-05-11 16:01:56.175][self$createEntryFromContent] Parsing 2 NCI CACTUS entries.
biodb.DEBUG[2024-05-11 16:01:56.176][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-11 16:01:56.177][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:01:56.177][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:01:56.182][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:56.183][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:56.183][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:56.184][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-11 16:01:56.189][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:56.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:56.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:56.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:56.193][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:56.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:56.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:56.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:56.197][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-11 16:01:56.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-11 16:01:56.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:56.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:56.200][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-11 16:01:56.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-11 16:01:56.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:56.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:56.203][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-11 16:01:56.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-11 16:01:56.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:56.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:56.206][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-11 16:01:56.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-11 16:01:56.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:56.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:56.210][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-11 16:01:56.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-11 16:01:56.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:56.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:56.214][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-11 16:01:56.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-11 16:01:56.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:56.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:56.217][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-11 16:01:56.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-11 16:01:56.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:56.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:56.221][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-11 16:01:56.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-11 16:01:56.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:56.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:56.224][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-05-11 16:01:56.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-05-11 16:01:56.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:56.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:56.227][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-05-11 16:01:56.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-05-11 16:01:56.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:56.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:56.231][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:56.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:56.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:56.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:56.234][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-05-11 16:01:56.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-05-11 16:01:56.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:56.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:56.237][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:56.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:56.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:56.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:56.240][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:56.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:56.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:56.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:56.243][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:56.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:56.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:56.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-11 16:01:56.246][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-11 16:01:56.247][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:01:56.247][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:01:56.252][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:56.253][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:56.254][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:56.254][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-11 16:01:56.267][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:56.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:56.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:56.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:56.270][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:56.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:56.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:56.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:56.274][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-05-11 16:01:56.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-05-11 16:01:56.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:56.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:56.277][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-05-11 16:01:56.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-05-11 16:01:56.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:56.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:56.281][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-11 16:01:56.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-11 16:01:56.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:56.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:56.284][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-11 16:01:56.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-11 16:01:56.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:56.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:56.287][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-11 16:01:56.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-11 16:01:56.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:56.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:56.290][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-11 16:01:56.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-11 16:01:56.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:56.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:56.294][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:01:56.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:01:56.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:56.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:56.297][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:01:56.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:01:56.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:56.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:56.300][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:01:56.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:01:56.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:56.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:56.303][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:01:56.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:01:56.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:56.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:56.306][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:01:56.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:01:56.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:56.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:56.309][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:01:56.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:01:56.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:56.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:56.312][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-11 16:01:56.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-11 16:01:56.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:56.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:56.316][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-11 16:01:56.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-11 16:01:56.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:56.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:56.319][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-11 16:01:56.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-11 16:01:56.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:56.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:56.323][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-11 16:01:56.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-11 16:01:56.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:56.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:56.326][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-11 16:01:56.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-11 16:01:56.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:56.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:56.330][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-05-11 16:01:56.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-05-11 16:01:56.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:56.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:56.333][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-05-11 16:01:56.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-05-11 16:01:56.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:56.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:56.336][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:56.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:56.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:56.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:56.339][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-05-11 16:01:56.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-05-11 16:01:56.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:56.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:56.343][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:56.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:56.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:56.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:56.346][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:56.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:56.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:56.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:56.349][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:56.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:56.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:56.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:56.353][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:56.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:56.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:56.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:56.356][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:56.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:56.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:56.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:56.359][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:56.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:56.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:56.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:56.362][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:56.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:56.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:56.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:56.366][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:56.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:56.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:56.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:56.369][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-11 16:01:56.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-11 16:01:56.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:56.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-11 16:01:56.372][self$createEntryFromContent] Accession numbers: 749674, 750690.
biodb.TRACE[2024-05-11 16:01:56.373][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-05-11 16:01:56.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-05-11 16:01:56.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:56.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:56.380][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-05-11 16:01:56.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-05-11 16:01:56.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:56.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:56.383][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-05-11 16:01:56.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-05-11 16:01:56.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:56.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:56.390][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-05-11 16:01:56.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-05-11 16:01:56.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:56.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:56.394][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-05-11 16:01:56.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-05-11 16:01:56.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:56.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:56.397][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-05-11 16:01:56.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-05-11 16:01:56.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:56.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-11 16:01:56.408][biodb::testThat]
biodb.INFO [2024-05-11 16:01:56.409][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-05-11 16:01:56.410][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-11 16:01:56.411][biodb::testThat]
biodb.INFO [2024-05-11 16:01:56.417][biodb::testThat]
biodb.INFO [2024-05-11 16:01:56.418][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-05-11 16:01:56.418][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-11 16:01:56.419][biodb::testThat]
biodb.WARN [2024-05-11 16:01:56.435][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2024-05-11 16:01:56.450][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2024-05-11 16:01:56.459][biodb::testThat]
biodb.INFO [2024-05-11 16:01:56.460][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-05-11 16:01:56.461][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-11 16:01:56.462][biodb::testThat]
biodb.TRACE[2024-05-11 16:01:56.482][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-11 16:01:56.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-11 16:01:56.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:56.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:56.485][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-11 16:01:56.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-11 16:01:56.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:56.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:56.488][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-11 16:01:56.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-11 16:01:56.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:56.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:56.492][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-11 16:01:56.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-11 16:01:56.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:56.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:56.523][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-11 16:01:56.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-11 16:01:56.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:56.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:56.526][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-11 16:01:56.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-11 16:01:56.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:56.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:56.529][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-11 16:01:56.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-11 16:01:56.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:56.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-11 16:01:56.532][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-11 16:01:56.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-11 16:01:56.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-11 16:01:56.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-11 16:01:56.541][biodb::testThat]
biodb.INFO [2024-05-11 16:01:56.542][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-05-11 16:01:56.543][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-11 16:01:56.543][biodb::testThat]
biodb.INFO [2024-05-11 16:01:56.550][biodb::testThat]
biodb.INFO [2024-05-11 16:01:56.551][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-05-11 16:01:56.552][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-11 16:01:56.553][biodb::testThat]
biodb.INFO [2024-05-11 16:01:56.560][biodb::testThat]
biodb.INFO [2024-05-11 16:01:56.560][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-05-11 16:01:56.561][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-11 16:01:56.562][biodb::testThat]
biodb.INFO [2024-05-11 16:01:56.568][biodb::testThat]
biodb.INFO [2024-05-11 16:01:56.568][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-05-11 16:01:56.569][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-11 16:01:56.570][biodb::testThat]
biodb.INFO [2024-05-11 16:01:56.576][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-05-11 16:01:56.577][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector nci.cactus from the request scheduler
biodb.INFO [2024-05-11 16:01:56.578][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2024-05-11 16:01:56.578][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-05-11 16:01:56.579][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:01:56.580][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:01:56.581][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:56.581][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:56.582][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:56.583][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-05-11 16:01:56.591][biodb::testContext]
biodb.INFO [2024-05-11 16:01:56.591][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-11 16:01:56.592][biodb::testContext] Test context - Example long tests
biodb.INFO [2024-05-11 16:01:56.593][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-11 16:01:56.594][biodb::testContext]
biodb.INFO [2024-05-11 16:01:56.595][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-05-11 16:01:56.597][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-05-11 16:01:56.600][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-11 16:01:56.601][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-05-11 16:01:56.602][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-05-11 16:01:56.602][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:56.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:56.604][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:56.604][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-05-11 16:01:56.605][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-05-11 16:01:56.606][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:56.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:56.607][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:56.608][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-05-11 16:01:56.609][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-05-11 16:01:56.610][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:56.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:56.616][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:56.616][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-05-11 16:01:56.617][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-05-11 16:01:56.618][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-05-11 16:01:56.619][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:56.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:56.620][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:56.621][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-05-11 16:01:56.622][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-05-11 16:01:56.622][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-05-11 16:01:56.623][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:56.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:56.625][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:56.625][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-05-11 16:01:56.626][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-05-11 16:01:56.627][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:56.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:56.628][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:56.629][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-05-11 16:01:56.629][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-05-11 16:01:56.630][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-05-11 16:01:56.631][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:56.632][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:56.632][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:56.633][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-05-11 16:01:56.634][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-05-11 16:01:56.634][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:56.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:56.636][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:56.636][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-05-11 16:01:56.637][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-05-11 16:01:56.638][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-05-11 16:01:56.639][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:56.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:56.640][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:56.641][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-05-11 16:01:56.642][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-05-11 16:01:56.642][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-05-11 16:01:56.643][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-05-11 16:01:56.644][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-05-11 16:01:56.645][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-05-11 16:01:56.645][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:56.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:56.647][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:56.647][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-05-11 16:01:56.648][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-05-11 16:01:56.649][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:56.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:56.650][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:56.651][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-05-11 16:01:56.652][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-05-11 16:01:56.653][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:56.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:56.654][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:56.655][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-05-11 16:01:56.656][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-05-11 16:01:56.656][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:56.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:56.658][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:56.659][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-05-11 16:01:56.659][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-05-11 16:01:56.660][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:56.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:56.662][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:56.662][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-05-11 16:01:56.663][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-05-11 16:01:56.664][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:56.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:56.665][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:56.666][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-05-11 16:01:56.667][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-05-11 16:01:56.687][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-05-11 16:01:56.688][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:56.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:56.689][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:56.690][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-05-11 16:01:56.691][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-05-11 16:01:56.692][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-05-11 16:01:56.693][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:56.693][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:56.694][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:56.695][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-05-11 16:01:56.696][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-11 16:01:56.697][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-05-11 16:01:56.698][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-11 16:01:56.699][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-11 16:01:56.700][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-11 16:01:56.700][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-11 16:01:56.701][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-11 16:01:56.702][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-11 16:01:56.703][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-11 16:01:56.704][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-11 16:01:56.705][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-11 16:01:56.705][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-05-11 16:01:56.706][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-11 16:01:56.707][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:01:56.708][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-11 16:01:56.709][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-11 16:01:56.709][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-11 16:01:56.709][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-11 16:01:56.709][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-11 16:01:56.709][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-11 16:01:56.710][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-11 16:01:56.711][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-11 16:01:56.711][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-11 16:01:56.712][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-11 16:01:56.713][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-11 16:01:56.714][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-11 16:01:56.714][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-11 16:01:56.715][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:01:56.716][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-11 16:01:56.717][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-11 16:01:56.718][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-11 16:01:56.719][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:01:56.720][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-05-11 16:01:56.721][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-11 16:01:56.722][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-05-11 16:01:56.723][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-11 16:01:56.724][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-11 16:01:56.725][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-11 16:01:56.725][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-11 16:01:56.726][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-11 16:01:56.727][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-11 16:01:56.728][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-11 16:01:56.729][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-11 16:01:56.729][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-11 16:01:56.730][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-05-11 16:01:56.731][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-11 16:01:56.732][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:01:56.733][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-11 16:01:56.733][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-11 16:01:56.733][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-11 16:01:56.733][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-11 16:01:56.733][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-11 16:01:56.733][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-11 16:01:56.734][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-11 16:01:56.735][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-11 16:01:56.736][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-11 16:01:56.737][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-11 16:01:56.737][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-11 16:01:56.738][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-11 16:01:56.739][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-11 16:01:56.740][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:01:56.740][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-11 16:01:56.741][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-11 16:01:56.742][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-11 16:01:56.747][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:01:56.748][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-05-11 16:01:56.749][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-11 16:01:56.750][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-05-11 16:01:56.751][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-11 16:01:56.751][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-11 16:01:56.752][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-11 16:01:56.753][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-11 16:01:56.754][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-11 16:01:56.755][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-11 16:01:56.755][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-11 16:01:56.756][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-11 16:01:56.757][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-11 16:01:56.758][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-05-11 16:01:56.759][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-11 16:01:56.759][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:01:56.760][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-11 16:01:56.761][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:01:56.762][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-11 16:01:56.762][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-11 16:01:56.763][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-11 16:01:56.764][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-11 16:01:56.765][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-11 16:01:56.765][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-11 16:01:56.766][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-11 16:01:56.767][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:01:56.768][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-11 16:01:56.768][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-11 16:01:56.769][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-11 16:01:56.770][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:01:56.771][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-05-11 16:01:56.772][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-11 16:01:56.773][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-05-11 16:01:56.774][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-11 16:01:56.775][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-11 16:01:56.776][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-11 16:01:56.776][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-11 16:01:56.777][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-11 16:01:56.778][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-11 16:01:56.779][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-11 16:01:56.780][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-11 16:01:56.780][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-11 16:01:56.781][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-05-11 16:01:56.782][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-11 16:01:56.783][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:01:56.784][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-11 16:01:56.784][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:01:56.785][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-11 16:01:56.786][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-11 16:01:56.787][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-11 16:01:56.788][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-11 16:01:56.788][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-11 16:01:56.789][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-11 16:01:56.790][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-11 16:01:56.791][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:01:56.791][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-11 16:01:56.792][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-11 16:01:56.793][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-11 16:01:56.794][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:01:56.795][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-11 16:01:56.796][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:56.796][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:56.797][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:56.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:56.799][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:56.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:56.800][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:56.801][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:56.802][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:56.802][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:56.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:56.804][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:56.804][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:56.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:56.806][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:56.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:56.807][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:56.808][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:56.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:56.810][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:56.810][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:56.811][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:56.812][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:56.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:56.813][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:56.814][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:56.815][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:56.816][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:56.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:56.817][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:56.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:56.818][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:56.819][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:56.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:56.820][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:56.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:56.822][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:56.823][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:56.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:56.824][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:56.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:56.825][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:56.826][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:56.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:56.827][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:56.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:56.829][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:56.830][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:56.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:56.831][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:56.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:56.832][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[2024-05-11 16:01:56.833][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:56.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:56.835][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:56.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:56.836][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[2024-05-11 16:01:56.837][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:56.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:56.838][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:56.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:56.840][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[2024-05-11 16:01:56.841][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:56.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:56.842][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:56.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:56.843][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:56.844][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:56.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:56.846][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:56.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:56.847][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:56.848][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:56.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:56.849][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:56.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:56.851][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:56.851][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:56.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:56.853][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:56.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:56.854][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:56.859][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:56.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:56.860][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:56.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:56.862][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:56.862][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-05-11 16:01:56.863][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-05-11 16:01:56.865][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-05-11 16:01:56.866][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-05-11 16:01:56.867][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-11 16:01:56.868][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-05-11 16:01:56.869][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-05-11 16:01:56.870][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-05-11 16:01:56.871][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-05-11 16:01:56.872][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-05-11 16:01:56.873][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-11 16:01:56.875][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-05-11 16:01:56.876][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-05-11 16:01:56.877][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-05-11 16:01:56.878][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-05-11 16:01:56.879][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-11 16:01:56.880][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-05-11 16:01:56.881][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-05-11 16:01:56.882][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-11 16:01:56.883][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-05-11 16:01:56.885][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-05-11 16:01:56.886][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-05-11 16:01:56.887][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-05-11 16:01:56.888][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-05-11 16:01:56.889][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-05-11 16:01:56.890][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-05-11 16:01:56.891][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-05-11 16:01:56.893][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-05-11 16:01:56.894][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-05-11 16:01:56.895][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-05-11 16:01:56.896][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-05-11 16:01:56.897][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-05-11 16:01:56.898][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-05-11 16:01:56.899][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-05-11 16:01:56.900][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-05-11 16:01:56.902][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-05-11 16:01:56.903][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-05-11 16:01:56.904][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-05-11 16:01:56.905][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-05-11 16:01:56.906][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-05-11 16:01:56.907][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-05-11 16:01:56.908][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-05-11 16:01:56.910][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-05-11 16:01:56.911][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-05-11 16:01:56.912][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-05-11 16:01:56.913][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-05-11 16:01:56.914][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-05-11 16:01:56.915][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-05-11 16:01:56.916][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-05-11 16:01:56.917][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-05-11 16:01:56.919][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-05-11 16:01:56.920][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-05-11 16:01:56.921][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-05-11 16:01:56.922][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-05-11 16:01:56.923][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-05-11 16:01:56.924][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-05-11 16:01:56.926][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-05-11 16:01:56.927][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-05-11 16:01:56.928][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-05-11 16:01:56.929][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-05-11 16:01:56.930][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-05-11 16:01:56.931][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-05-11 16:01:56.932][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-05-11 16:01:56.934][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-05-11 16:01:56.935][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-05-11 16:01:56.936][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-05-11 16:01:56.937][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-11 16:01:56.938][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-11 16:01:56.939][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-05-11 16:01:56.940][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-05-11 16:01:56.942][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-05-11 16:01:56.943][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-05-11 16:01:56.944][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-05-11 16:01:56.945][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-05-11 16:01:56.946][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-05-11 16:01:56.947][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-05-11 16:01:56.948][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-05-11 16:01:56.950][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-05-11 16:01:56.951][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-05-11 16:01:56.952][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-05-11 16:01:56.953][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-05-11 16:01:56.954][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-05-11 16:01:56.955][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-05-11 16:01:56.956][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-05-11 16:01:56.958][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-05-11 16:01:56.959][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-11 16:01:56.959][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:56.960][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:56.961][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:56.962][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:56.962][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:56.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:01:56.964][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:01:56.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:56.965][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:56.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:56.972][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:56.972][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:56.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:01:56.974][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:01:56.974][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:56.975][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:56.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:56.977][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[2024-05-11 16:01:56.977][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:56.978][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:01:56.979][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:01:56.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:56.980][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:56.981][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:56.982][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:56.982][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:56.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:01:56.984][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:01:56.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:56.985][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:56.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:56.986][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:56.987][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:56.988][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:01:56.989][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:01:56.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:56.990][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:56.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:56.991][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:56.992][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:56.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:01:56.994][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:01:56.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:56.995][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:56.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:56.996][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:56.997][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:56.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:01:56.998][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:01:56.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:57.000][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:57.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:57.001][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:57.002][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:57.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:01:57.003][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:01:57.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:57.005][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:57.006][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:57.006][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:57.007][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:57.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:01:57.009][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:01:57.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:57.010][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:57.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:57.011][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:57.012][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:57.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:01:57.014][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:01:57.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:57.015][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:57.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:57.016][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:57.017][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:57.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:01:57.018][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:01:57.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:57.020][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:57.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:57.021][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:57.022][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:57.023][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:01:57.023][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:01:57.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:57.025][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:57.025][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:57.026][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:57.027][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:57.027][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:01:57.028][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:01:57.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:57.030][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:57.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:57.031][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:57.032][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:57.033][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:01:57.033][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:01:57.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:57.035][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:57.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:57.036][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:57.037][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:57.037][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:01:57.038][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:01:57.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:57.040][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:57.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:57.041][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:57.042][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:57.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:01:57.043][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:01:57.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:57.045][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:57.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:57.046][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:57.047][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-11 16:01:57.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:01:57.048][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:01:57.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:57.050][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:57.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:57.051][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-11 16:01:57.053][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.19-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2024-05-11 16:01:57.054][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2024-05-11 16:01:57.056][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-11 16:01:57.057][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2024-05-11 16:01:57.058][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-11 16:01:57.058][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-11 16:01:57.059][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2024-05-11 16:01:57.060][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2024-05-11 16:01:57.061][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-05-11 16:01:57.062][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-11 16:01:57.062][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2024-05-11 16:01:57.063][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-11 16:01:57.064][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-11 16:01:57.065][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2024-05-11 16:01:57.066][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-11 16:01:57.066][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2024-05-11 16:01:57.066][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2024-05-11 16:01:57.066][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2024-05-11 16:01:57.066][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2024-05-11 16:01:57.066][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2024-05-11 16:01:57.066][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2024-05-11 16:01:57.066][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2024-05-11 16:01:57.067][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-05-11 16:01:57.068][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:01:57.069][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-05-11 16:01:57.070][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-11 16:01:57.071][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-11 16:01:57.071][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-11 16:01:57.072][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-11 16:01:57.073][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-11 16:01:57.074][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-11 16:01:57.074][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2024-05-11 16:01:57.074][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2024-05-11 16:01:57.074][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2024-05-11 16:01:57.074][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2024-05-11 16:01:57.075][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-11 16:01:57.076][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-11 16:01:57.077][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-05-11 16:01:57.078][self$setPropertyValue]
biodb.DEBUG[2024-05-11 16:01:57.083][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2024-05-11 16:01:57.085][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2024-05-11 16:01:57.086][super$initialize] Register connector nci.cactus with the request scheduler
biodb.DEBUG[2024-05-11 16:01:57.087][private$bdb$getRequestScheduler()$re ...] Register connector nci.cactus.
biodb.DEBUG[2024-05-11 16:01:57.088][private$addConnectorRules] Create new rule for URL "cactus.nci.nih.gov" of connector "nci.cactus".
biodb.DEBUG[2024-05-11 16:01:57.089][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-11 16:01:57.090][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-11 16:01:57.091][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-05-11 16:01:57.092][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-05-11 16:01:57.093][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-05-11 16:01:57.094][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2024-05-11 16:01:57.095][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-05-11 16:01:57.096][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector nci.cactus from the request scheduler
biodb.INFO [2024-05-11 16:01:57.097][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2024-05-11 16:01:57.097][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-05-11 16:01:57.098][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-11 16:01:57.099][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-11 16:01:57.100][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-11 16:01:57.100][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-11 16:01:57.101][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-05-11 16:01:57.102][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".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 92 ]
> 
> proc.time()
   user  system elapsed 
  3.781   0.269   4.097

'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)