Back to Long Tests report for BioC 3.20

This page was generated on 2024-09-21 23:55 -0400 (Sat, 21 Sep 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4438
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4451
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4484
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 8/32HostnameOS / ArchCHECK
biodbHmdb 1.11.0  (landing page)
Pierrick Roger
Snapshot Date: 2024-09-21 09:55 -0400 (Sat, 21 Sep 2024)
git_url: https://git.bioconductor.org/packages/biodbHmdb
git_branch: devel
git_last_commit: c3d59a4
git_last_commit_date: 2024-04-30 11:39:05 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  ERROR  
palomino8Windows Server 2022 Datacenter / x64  ERROR  
lconwaymacOS 12.7.1 Monterey / x86_64  WARNINGS  

CHECK results for biodbHmdb on palomino8

To the developers/maintainers of the biodbHmdb 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: biodbHmdb
Version: 1.11.0
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbHmdb_1.11.0.tar.gz
StartedAt: 2024-09-21 16:02:35 -0400 (Sat, 21 Sep 2024)
EndedAt: 2024-09-21 16:53:17 -0400 (Sat, 21 Sep 2024)
EllapsedTime: 3041.9 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbHmdb.Rcheck
Warnings: NA

Tests output

biodbHmdb.Rcheck/tests/testthat.Rout.fail


R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbHmdb)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbHmdb")
biodb.INFO [2024-09-21 16:04:09.582][biodb::testContext]
biodb.INFO [2024-09-21 16:04:09.585][biodb::testContext] ********************************************************************************
biodb.INFO [2024-09-21 16:04:09.587][biodb::testContext] Test context - Generic long tests
biodb.INFO [2024-09-21 16:04:09.588][biodb::testContext] ********************************************************************************
biodb.INFO [2024-09-21 16:04:09.589][biodb::testContext]
biodb.INFO [2024-09-21 16:04:09.595][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.13.0.
biodb.DEBUG[2024-09-21 16:04:09.598][self$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.20-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2024-09-21 16:04:09.605][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-09-21 16:04:09.606][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-09-21 16:04:09.608][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-09-21 16:04:09.609][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:04:09.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:04:09.611][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-21 16:04:09.612][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-09-21 16:04:09.628][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-09-21 16:04:09.629][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:04:09.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:04:09.631][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-21 16:04:09.632][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-09-21 16:04:09.634][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-09-21 16:04:09.635][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:04:09.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:04:09.637][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-21 16:04:09.638][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-09-21 16:04:09.639][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-09-21 16:04:09.640][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-09-21 16:04:09.641][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:04:09.642][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:04:09.644][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-21 16:04:09.645][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-09-21 16:04:09.646][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-09-21 16:04:09.647][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-09-21 16:04:09.648][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:04:09.649][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:04:09.650][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-21 16:04:09.651][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-09-21 16:04:09.653][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-09-21 16:04:09.654][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:04:09.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:04:09.656][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[2024-09-21 16:04:09.657][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-09-21 16:04:09.658][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-09-21 16:04:09.659][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-09-21 16:04:09.660][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:04:09.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:04:09.662][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-21 16:04:09.664][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-09-21 16:04:09.665][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-09-21 16:04:09.666][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:04:09.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:04:09.668][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-21 16:04:09.669][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-09-21 16:04:09.670][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-09-21 16:04:09.672][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-09-21 16:04:09.673][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:04:09.674][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:04:09.675][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-21 16:04:09.676][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-09-21 16:04:09.677][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-09-21 16:04:09.678][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-09-21 16:04:09.680][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-09-21 16:04:09.681][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-09-21 16:04:09.682][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-09-21 16:04:09.683][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:04:09.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:04:09.685][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-21 16:04:09.686][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-09-21 16:04:09.688][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-09-21 16:04:09.689][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:04:09.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:04:09.691][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-21 16:04:09.692][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-09-21 16:04:09.693][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-09-21 16:04:09.694][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:04:09.695][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:04:09.696][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-21 16:04:09.697][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-09-21 16:04:09.699][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-09-21 16:04:09.700][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:04:09.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:04:09.702][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-21 16:04:09.703][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-09-21 16:04:09.704][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-09-21 16:04:09.705][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:04:09.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:04:09.707][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-21 16:04:09.708][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-09-21 16:04:09.710][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-09-21 16:04:09.711][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:04:09.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:04:09.713][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-21 16:04:09.714][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-09-21 16:04:09.715][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-09-21 16:04:09.719][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-09-21 16:04:09.720][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:04:09.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:04:09.722][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-21 16:04:09.723][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-09-21 16:04:09.724][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-09-21 16:04:09.726][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-09-21 16:04:09.727][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:04:09.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:04:09.729][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-21 16:04:09.732][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-09-21 16:04:09.766][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-09-21 16:04:09.780][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-09-21 16:04:09.782][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-09-21 16:04:09.783][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-09-21 16:04:09.784][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-09-21 16:04:09.785][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-09-21 16:04:09.786][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-09-21 16:04:09.787][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-09-21 16:04:09.789][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-09-21 16:04:09.790][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-09-21 16:04:09.791][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-09-21 16:04:09.792][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-09-21 16:04:09.794][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-09-21 16:04:09.795][self$setPropertyValue]
biodb.DEBUG[2024-09-21 16:04:09.796][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-09-21 16:04:09.797][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-09-21 16:04:09.797][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-09-21 16:04:09.797][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-09-21 16:04:09.797][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-09-21 16:04:09.797][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-09-21 16:04:09.798][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-09-21 16:04:09.800][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-21 16:04:09.801][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-21 16:04:09.802][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-09-21 16:04:09.803][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-21 16:04:09.804][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-21 16:04:09.805][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-09-21 16:04:09.806][self$setPropertyValue]
biodb.DEBUG[2024-09-21 16:04:09.807][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-09-21 16:04:09.809][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-09-21 16:04:09.810][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-09-21 16:04:09.811][self$setPropertyValue]
biodb.DEBUG[2024-09-21 16:04:09.812][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-09-21 16:04:09.814][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-09-21 16:04:09.815][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-09-21 16:04:09.817][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-09-21 16:04:09.818][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-09-21 16:04:09.819][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-09-21 16:04:09.820][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-09-21 16:04:09.821][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-09-21 16:04:09.823][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-09-21 16:04:09.824][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-09-21 16:04:09.825][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-09-21 16:04:09.826][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-09-21 16:04:09.827][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-09-21 16:04:09.828][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-09-21 16:04:09.830][self$setPropertyValue]
biodb.DEBUG[2024-09-21 16:04:09.831][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-09-21 16:04:09.832][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-09-21 16:04:09.832][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-09-21 16:04:09.832][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-09-21 16:04:09.832][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-09-21 16:04:09.832][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-09-21 16:04:09.833][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-09-21 16:04:09.834][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-21 16:04:09.836][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-21 16:04:09.837][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-09-21 16:04:09.838][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-21 16:04:09.839][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-21 16:04:09.840][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-09-21 16:04:09.841][self$setPropertyValue]
biodb.DEBUG[2024-09-21 16:04:09.842][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-09-21 16:04:09.844][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-09-21 16:04:09.845][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-09-21 16:04:09.846][self$setPropertyValue]
biodb.DEBUG[2024-09-21 16:04:09.847][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-09-21 16:04:09.849][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-09-21 16:04:09.850][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-09-21 16:04:09.852][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-09-21 16:04:09.853][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-09-21 16:04:09.854][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-09-21 16:04:09.855][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-09-21 16:04:09.856][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-09-21 16:04:09.858][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-09-21 16:04:09.859][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-09-21 16:04:09.860][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-09-21 16:04:09.861][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-09-21 16:04:09.862][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-09-21 16:04:09.864][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-09-21 16:04:09.865][self$setPropertyValue]
biodb.DEBUG[2024-09-21 16:04:09.866][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-09-21 16:04:09.867][self$setPropertyValue]
biodb.DEBUG[2024-09-21 16:04:09.868][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-09-21 16:04:09.869][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-21 16:04:09.870][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-21 16:04:09.872][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-09-21 16:04:09.873][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-21 16:04:09.874][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-21 16:04:09.875][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-09-21 16:04:09.876][self$setPropertyValue]
biodb.DEBUG[2024-09-21 16:04:09.877][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-09-21 16:04:09.878][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-09-21 16:04:09.880][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-09-21 16:04:09.881][self$setPropertyValue]
biodb.DEBUG[2024-09-21 16:04:09.882][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-09-21 16:04:09.884][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-09-21 16:04:09.885][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-09-21 16:04:09.887][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-09-21 16:04:09.888][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-09-21 16:04:09.889][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-09-21 16:04:09.890][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-09-21 16:04:09.891][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-09-21 16:04:09.892][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-09-21 16:04:09.894][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-09-21 16:04:09.895][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-09-21 16:04:09.896][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-09-21 16:04:09.897][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-09-21 16:04:09.898][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-09-21 16:04:09.900][self$setPropertyValue]
biodb.DEBUG[2024-09-21 16:04:09.901][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-09-21 16:04:09.902][self$setPropertyValue]
biodb.DEBUG[2024-09-21 16:04:09.903][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-09-21 16:04:09.904][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-21 16:04:09.905][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-21 16:04:09.907][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-09-21 16:04:09.908][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-21 16:04:09.909][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-21 16:04:09.910][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-09-21 16:04:09.911][self$setPropertyValue]
biodb.DEBUG[2024-09-21 16:04:09.912][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-09-21 16:04:09.913][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-09-21 16:04:09.915][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-09-21 16:04:09.916][self$setPropertyValue]
biodb.DEBUG[2024-09-21 16:04:09.919][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-09-21 16:04:09.920][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:04:09.921][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-21 16:04:09.922][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:04:09.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-21 16:04:09.924][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-21 16:04:09.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:04:09.927][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-21 16:04:09.928][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:04:09.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-21 16:04:09.930][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-21 16:04:09.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:04:09.932][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-21 16:04:09.933][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:04:09.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-21 16:04:09.935][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-21 16:04:09.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:04:09.937][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-21 16:04:09.939][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:04:09.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-21 16:04:09.941][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-21 16:04:09.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:04:09.943][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-21 16:04:09.944][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:04:09.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-21 16:04:09.946][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-21 16:04:09.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:04:09.948][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-21 16:04:09.949][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:04:09.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-21 16:04:09.956][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-21 16:04:09.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:04:09.959][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-21 16:04:09.960][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:04:09.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-21 16:04:09.962][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-21 16:04:09.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:04:09.964][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-21 16:04:09.965][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:04:09.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-21 16:04:09.967][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-21 16:04:09.968][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:04:09.969][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-21 16:04:09.970][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:04:09.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-21 16:04:09.972][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-21 16:04:09.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:04:09.975][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-21 16:04:09.976][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:04:09.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-21 16:04:09.978][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-21 16:04:09.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:04:09.980][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-21 16:04:09.981][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:04:09.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-21 16:04:09.983][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-21 16:04:09.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:04:09.985][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-21 16:04:09.986][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:04:09.988][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-21 16:04:09.989][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-21 16:04:09.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:04:09.991][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[2024-09-21 16:04:09.992][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:04:09.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-21 16:04:09.994][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-21 16:04:09.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:04:09.996][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[2024-09-21 16:04:09.997][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:04:09.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-21 16:04:09.999][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-21 16:04:10.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:04:10.002][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-21 16:04:10.003][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:04:10.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-21 16:04:10.005][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-21 16:04:10.006][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:04:10.007][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-21 16:04:10.008][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:04:10.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-21 16:04:10.010][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-21 16:04:10.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:04:10.013][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-21 16:04:10.014][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:04:10.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-21 16:04:10.016][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-21 16:04:10.017][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:04:10.018][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-21 16:04:10.019][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-09-21 16:04:10.023][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-09-21 16:04:10.025][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-09-21 16:04:10.026][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-09-21 16:04:10.028][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-09-21 16:04:10.029][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-09-21 16:04:10.031][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-09-21 16:04:10.033][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-09-21 16:04:10.034][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-09-21 16:04:10.036][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-09-21 16:04:10.037][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-09-21 16:04:10.039][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-09-21 16:04:10.040][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-09-21 16:04:10.042][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-09-21 16:04:10.043][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-09-21 16:04:10.045][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-09-21 16:04:10.047][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-09-21 16:04:10.048][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-09-21 16:04:10.050][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-09-21 16:04:10.051][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-09-21 16:04:10.053][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-09-21 16:04:10.054][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-09-21 16:04:10.056][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-09-21 16:04:10.057][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-09-21 16:04:10.059][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-09-21 16:04:10.061][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-09-21 16:04:10.062][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-09-21 16:04:10.064][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-09-21 16:04:10.065][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-09-21 16:04:10.067][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-09-21 16:04:10.068][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-09-21 16:04:10.070][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-09-21 16:04:10.072][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-09-21 16:04:10.073][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-09-21 16:04:10.075][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-09-21 16:04:10.076][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-09-21 16:04:10.078][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-09-21 16:04:10.079][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-09-21 16:04:10.081][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-09-21 16:04:10.082][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-09-21 16:04:10.084][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-09-21 16:04:10.086][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-09-21 16:04:10.087][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-09-21 16:04:10.089][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-09-21 16:04:10.090][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-09-21 16:04:10.092][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-09-21 16:04:10.094][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-09-21 16:04:10.095][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-09-21 16:04:10.097][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-09-21 16:04:10.098][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-09-21 16:04:10.100][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-09-21 16:04:10.102][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-09-21 16:04:10.103][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-09-21 16:04:10.105][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-09-21 16:04:10.106][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-09-21 16:04:10.108][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-09-21 16:04:10.109][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-09-21 16:04:10.111][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-09-21 16:04:10.112][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-09-21 16:04:10.114][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-09-21 16:04:10.116][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-09-21 16:04:10.117][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-09-21 16:04:10.119][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-09-21 16:04:10.120][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-09-21 16:04:10.122][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-09-21 16:04:10.123][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-09-21 16:04:10.125][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-09-21 16:04:10.127][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-09-21 16:04:10.128][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-09-21 16:04:10.130][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-09-21 16:04:10.131][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-09-21 16:04:10.133][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-09-21 16:04:10.134][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-09-21 16:04:10.136][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-09-21 16:04:10.138][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-09-21 16:04:10.139][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-09-21 16:04:10.141][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-09-21 16:04:10.142][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-09-21 16:04:10.144][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-09-21 16:04:10.145][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-09-21 16:04:10.147][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-09-21 16:04:10.149][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-09-21 16:04:10.150][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-09-21 16:04:10.190][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-09-21 16:04:10.193][initialize] This is biodb version 1.13.0.
biodb.DEBUG[2024-09-21 16:04:10.196][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-09-21 16:04:10.197][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-09-21 16:04:10.198][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-21 16:04:10.199][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:04:10.200][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-21 16:04:10.205][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:04:10.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-21 16:04:10.207][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-21 16:04:10.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-21 16:04:10.209][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-21 16:04:10.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:04:10.211][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-21 16:04:10.212][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:04:10.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-21 16:04:10.214][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-21 16:04:10.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-21 16:04:10.217][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-21 16:04:10.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:04:10.219][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-21 16:04:10.220][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:04:10.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-21 16:04:10.222][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-21 16:04:10.223][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-21 16:04:10.224][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-21 16:04:10.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:04:10.226][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-21 16:04:10.227][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:04:10.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-21 16:04:10.229][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-21 16:04:10.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-21 16:04:10.232][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-21 16:04:10.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:04:10.234][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-21 16:04:10.235][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:04:10.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-21 16:04:10.237][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-21 16:04:10.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-21 16:04:10.239][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-21 16:04:10.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:04:10.241][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-21 16:04:10.242][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:04:10.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-21 16:04:10.244][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-21 16:04:10.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-21 16:04:10.246][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-21 16:04:10.248][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:04:10.249][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-21 16:04:10.250][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:04:10.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-21 16:04:10.252][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-21 16:04:10.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-21 16:04:10.254][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-21 16:04:10.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:04:10.256][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-21 16:04:10.257][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:04:10.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-21 16:04:10.259][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-21 16:04:10.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-21 16:04:10.261][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-21 16:04:10.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:04:10.264][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-21 16:04:10.265][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:04:10.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-21 16:04:10.267][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-21 16:04:10.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-21 16:04:10.269][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-21 16:04:10.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:04:10.271][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-21 16:04:10.272][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:04:10.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-21 16:04:10.274][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-21 16:04:10.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-21 16:04:10.276][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-21 16:04:10.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:04:10.279][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-21 16:04:10.280][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:04:10.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-21 16:04:10.282][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-21 16:04:10.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-21 16:04:10.284][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-21 16:04:10.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:04:10.286][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-21 16:04:10.287][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:04:10.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-21 16:04:10.289][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-21 16:04:10.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-21 16:04:10.291][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-21 16:04:10.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:04:10.294][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-21 16:04:10.295][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:04:10.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-21 16:04:10.297][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-21 16:04:10.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-21 16:04:10.299][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-21 16:04:10.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:04:10.301][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-21 16:04:10.302][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:04:10.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-21 16:04:10.304][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-21 16:04:10.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-21 16:04:10.306][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-21 16:04:10.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:04:10.309][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-21 16:04:10.310][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:04:10.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-21 16:04:10.312][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-21 16:04:10.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-21 16:04:10.314][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-21 16:04:10.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:04:10.316][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-21 16:04:10.317][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:04:10.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-21 16:04:10.319][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-21 16:04:10.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-21 16:04:10.321][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-21 16:04:10.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:04:10.324][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-21 16:04:10.325][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:04:10.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-21 16:04:10.327][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-21 16:04:10.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-21 16:04:10.329][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-21 16:04:10.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:04:10.331][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-21 16:04:10.332][biodb$getConfig()$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-09-21 16:04:10.333][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-09-21 16:04:10.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-21 16:04:10.336][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-21 16:04:10.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-21 16:04:10.338][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-21 16:04:10.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:04:10.340][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-09-21 16:04:10.343][biodb$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.20-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/definitions.yml".
biodb.DEBUG[2024-09-21 16:04:10.352][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2024-09-21 16:04:10.354][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-09-21 16:04:10.355][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-09-21 16:04:10.356][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-09-21 16:04:10.357][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-09-21 16:04:10.359][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2024-09-21 16:04:10.360][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2024-09-21 16:04:10.361][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-09-21 16:04:10.362][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-09-21 16:04:10.363][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-09-21 16:04:10.365][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-09-21 16:04:10.366][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-09-21 16:04:10.367][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2024-09-21 16:04:10.368][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-09-21 16:04:10.369][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2024-09-21 16:04:10.369][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2024-09-21 16:04:10.369][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2024-09-21 16:04:10.369][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2024-09-21 16:04:10.369][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2024-09-21 16:04:10.369][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2024-09-21 16:04:10.369][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2024-09-21 16:04:10.369][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2024-09-21 16:04:10.369][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2024-09-21 16:04:10.369][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2024-09-21 16:04:10.369][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2024-09-21 16:04:10.369][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2024-09-21 16:04:10.369][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2024-09-21 16:04:10.369][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2024-09-21 16:04:10.369][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2024-09-21 16:04:10.369][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2024-09-21 16:04:10.369][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2024-09-21 16:04:10.369][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2024-09-21 16:04:10.371][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-09-21 16:04:10.372][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-09-21 16:04:10.372][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2024-09-21 16:04:10.372][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2024-09-21 16:04:10.373][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-09-21 16:04:10.375][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-21 16:04:10.376][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-21 16:04:10.377][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-09-21 16:04:10.378][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-09-21 16:04:10.379][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-09-21 16:04:10.380][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-09-21 16:04:10.381][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2024-09-21 16:04:10.381][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2024-09-21 16:04:10.383][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-09-21 16:04:10.384][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-09-21 16:04:10.385][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-09-21 16:04:10.386][self$setPropertyValue]
biodb.DEBUG[2024-09-21 16:04:10.418][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2024-09-21 16:04:10.420][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-09-21 16:04:10.422][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-09-21 16:04:10.424][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-09-21 16:04:10.425][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-09-21 16:04:10.448][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2024-09-21 16:04:10.450][initialize] Register connector hmdb.metabolites with the request scheduler
biodb.DEBUG[2024-09-21 16:04:10.453][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites.
biodb.DEBUG[2024-09-21 16:04:10.457][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2024-09-21 16:04:10.461][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-09-21 16:04:10.462][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-09-21 16:04:10.464][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca".
biodb.DEBUG[2024-09-21 16:04:10.465][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.INFO [2024-09-21 16:04:10.475][biodb::testThat]
biodb.INFO [2024-09-21 16:04:10.476][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-09-21 16:04:10.477][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-21 16:04:10.478][biodb::testThat]
biodb.TRACE[2024-09-21 16:04:10.484][loadFileContents] Loaded 1 files from cache: [1]: "F:/biocbuild/bbs-3.20-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/testref/entry-hmdb.metabolites-HMDB0000001-content.xml".
biodb.DEBUG[2024-09-21 16:04:10.486][biodb$getFactory()$createEntryFromCo ...] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2024-09-21 16:04:10.489][biodb$getFactory()$createEntryFromCo ...] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2024-09-21 16:04:10.496][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-21 16:04:10.497][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-21 16:04:10.498][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-21 16:04:10.514][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-21 16:04:10.515][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-21 16:04:10.517][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:04:10.518][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-21 16:04:10.528][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-21 16:04:10.530][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-21 16:04:10.531][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:10.532][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:10.534][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-21 16:04:10.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-21 16:04:10.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:10.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:10.549][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-09-21 16:04:10.550][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-09-21 16:04:10.551][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:10.552][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:10.576][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-09-21 16:04:10.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-09-21 16:04:10.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:10.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:10.581][ef$get] Asked field names are: average.mass.
biodb.TRACE[2024-09-21 16:04:10.583][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-09-21 16:04:10.584][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:10.585][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:10.587][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-09-21 16:04:10.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-09-21 16:04:10.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:10.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:10.592][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-09-21 16:04:10.593][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-09-21 16:04:10.594][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:10.595][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:10.597][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-09-21 16:04:10.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-09-21 16:04:10.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:10.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:10.602][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-21 16:04:10.603][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-21 16:04:10.605][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:10.606][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:10.607][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-21 16:04:10.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-21 16:04:10.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:10.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:10.612][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-09-21 16:04:10.614][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-09-21 16:04:10.615][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:10.616][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:10.618][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-09-21 16:04:10.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-09-21 16:04:10.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:10.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:10.634][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-21 16:04:10.635][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-21 16:04:10.636][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:10.637][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:10.639][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-21 16:04:10.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-21 16:04:10.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:10.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:10.644][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-21 16:04:10.645][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-21 16:04:10.646][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:10.647][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:10.649][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-21 16:04:10.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-21 16:04:10.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:10.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:10.654][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-09-21 16:04:10.655][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-09-21 16:04:10.656][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:10.657][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:10.659][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-09-21 16:04:10.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-09-21 16:04:10.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:10.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:10.664][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-09-21 16:04:10.665][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-09-21 16:04:10.667][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:10.668][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:10.669][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-09-21 16:04:10.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-09-21 16:04:10.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:10.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:10.674][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-21 16:04:10.675][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-21 16:04:10.677][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:10.678][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:10.679][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-21 16:04:10.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-21 16:04:10.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:10.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:10.684][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-21 16:04:10.685][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-21 16:04:10.687][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:10.688][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:10.689][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-21 16:04:10.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-21 16:04:10.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:10.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:10.694][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-21 16:04:10.696][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-21 16:04:10.697][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:10.698][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:10.699][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-21 16:04:10.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-21 16:04:10.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:10.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:10.704][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-21 16:04:10.706][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-21 16:04:10.707][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:10.708][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:10.709][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-21 16:04:10.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-21 16:04:10.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:10.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:10.714][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-21 16:04:10.716][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-21 16:04:10.717][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:10.718][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:10.719][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-21 16:04:10.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-21 16:04:10.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:10.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:10.724][ef$get] Asked field names are: description.
biodb.TRACE[2024-09-21 16:04:10.726][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-09-21 16:04:10.727][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:10.728][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:10.729][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-09-21 16:04:10.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-09-21 16:04:10.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:10.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:10.734][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-21 16:04:10.736][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-21 16:04:10.737][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:10.738][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:10.739][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-21 16:04:10.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-21 16:04:10.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:10.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:10.744][ef$get] Asked field names are: super.class.
biodb.TRACE[2024-09-21 16:04:10.746][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-09-21 16:04:10.747][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:10.748][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:10.750][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2024-09-21 16:04:10.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-09-21 16:04:10.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:10.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:10.755][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-21 16:04:10.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-21 16:04:10.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:10.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:10.759][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-21 16:04:10.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-21 16:04:10.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:10.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:10.764][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-21 16:04:10.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-21 16:04:10.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:10.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:10.802][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-09-21 16:04:10.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-09-21 16:04:10.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:10.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:10.807][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-09-21 16:04:10.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-09-21 16:04:10.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:10.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:10.812][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-09-21 16:04:10.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-09-21 16:04:10.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:10.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:10.817][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-09-21 16:04:10.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-09-21 16:04:10.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:10.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:10.822][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-09-21 16:04:10.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-09-21 16:04:10.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:10.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:10.827][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-09-21 16:04:10.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-09-21 16:04:10.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:10.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:10.832][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-21 16:04:10.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-21 16:04:10.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:10.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:10.836][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-21 16:04:10.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-21 16:04:10.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:10.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:10.841][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-21 16:04:10.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-21 16:04:10.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:10.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:10.846][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-09-21 16:04:10.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-09-21 16:04:10.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:10.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:10.851][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-09-21 16:04:10.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-09-21 16:04:10.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:10.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:10.856][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-09-21 16:04:10.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-09-21 16:04:10.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:10.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:10.860][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-09-21 16:04:10.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-09-21 16:04:10.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:10.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:10.865][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-09-21 16:04:10.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-09-21 16:04:10.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:10.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:10.870][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-09-21 16:04:10.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-09-21 16:04:10.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:10.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:10.875][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-09-21 16:04:10.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-09-21 16:04:10.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:10.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:10.880][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-09-21 16:04:10.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-09-21 16:04:10.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:10.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:10.885][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-09-21 16:04:10.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-09-21 16:04:10.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:10.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:10.889][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-09-21 16:04:10.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-09-21 16:04:10.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:10.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:10.894][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-09-21 16:04:10.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-09-21 16:04:10.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:10.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:10.899][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-09-21 16:04:10.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-09-21 16:04:10.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:10.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:10.904][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-09-21 16:04:10.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-09-21 16:04:10.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:10.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:10.909][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-09-21 16:04:10.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-09-21 16:04:10.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:10.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:10.913][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-09-21 16:04:10.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-09-21 16:04:10.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:10.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:10.918][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-21 16:04:10.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-21 16:04:10.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:10.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:10.923][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-21 16:04:10.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-21 16:04:10.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:10.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:10.928][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-21 16:04:10.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-21 16:04:10.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:10.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:10.933][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-21 16:04:10.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-21 16:04:10.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:10.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:10.937][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-21 16:04:10.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-21 16:04:10.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:10.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:10.942][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-21 16:04:10.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-21 16:04:10.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:10.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:10.947][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-21 16:04:10.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-21 16:04:10.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:10.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:10.952][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-21 16:04:10.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-21 16:04:10.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:10.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:10.957][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-21 16:04:10.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-21 16:04:10.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:10.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:10.962][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-21 16:04:10.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-21 16:04:10.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:10.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:10.971][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-21 16:04:10.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-21 16:04:10.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:10.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:10.976][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-21 16:04:10.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-21 16:04:10.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:10.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:10.981][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-21 16:04:10.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-21 16:04:10.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:10.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:10.985][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-21 16:04:10.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-21 16:04:10.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:10.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:10.990][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-21 16:04:10.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-21 16:04:10.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:10.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:10.995][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-21 16:04:10.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-21 16:04:10.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:10.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.000][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-21 16:04:11.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-21 16:04:11.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.005][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-21 16:04:11.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-21 16:04:11.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.010][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-21 16:04:11.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-21 16:04:11.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.015][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-21 16:04:11.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-21 16:04:11.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.019][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-21 16:04:11.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-21 16:04:11.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.024][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-09-21 16:04:11.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-09-21 16:04:11.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.029][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-09-21 16:04:11.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-09-21 16:04:11.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.034][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-09-21 16:04:11.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-09-21 16:04:11.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.039][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-21 16:04:11.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-21 16:04:11.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.043][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-21 16:04:11.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-21 16:04:11.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.048][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-21 16:04:11.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-21 16:04:11.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.053][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2024-09-21 16:04:11.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-21 16:04:11.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.058][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-21 16:04:11.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-21 16:04:11.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.063][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-21 16:04:11.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-21 16:04:11.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.067][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-21 16:04:11.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-21 16:04:11.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.072][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2024-09-21 16:04:11.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-21 16:04:11.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.092][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-21 16:04:11.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-21 16:04:11.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.098][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-21 16:04:11.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-21 16:04:11.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.103][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-21 16:04:11.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-21 16:04:11.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.107][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-21 16:04:11.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-21 16:04:11.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.112][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-21 16:04:11.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-21 16:04:11.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.117][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-09-21 16:04:11.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-09-21 16:04:11.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.122][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-09-21 16:04:11.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-09-21 16:04:11.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.127][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-21 16:04:11.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-21 16:04:11.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.132][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-09-21 16:04:11.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-09-21 16:04:11.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.141][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-21 16:04:11.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-21 16:04:11.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.146][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-21 16:04:11.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-21 16:04:11.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.151][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-21 16:04:11.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-21 16:04:11.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.156][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-21 16:04:11.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-21 16:04:11.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.161][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-21 16:04:11.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-21 16:04:11.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.166][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-21 16:04:11.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-21 16:04:11.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-21 16:04:11.171][biodb$getFactory()$createEntryFromCo ...] Accession numbers: HMDB0000001.
biodb.TRACE[2024-09-21 16:04:11.174][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-09-21 16:04:11.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-09-21 16:04:11.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.179][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-09-21 16:04:11.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-09-21 16:04:11.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.184][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-09-21 16:04:11.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-09-21 16:04:11.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.189][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-09-21 16:04:11.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-09-21 16:04:11.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.215][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-21 16:04:11.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-21 16:04:11.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.233][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-09-21 16:04:11.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-09-21 16:04:11.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.244][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-21 16:04:11.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-21 16:04:11.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.249][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-21 16:04:11.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-21 16:04:11.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.254][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-21 16:04:11.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-21 16:04:11.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.260][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-21 16:04:11.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-21 16:04:11.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.265][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-21 16:04:11.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-21 16:04:11.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.270][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-21 16:04:11.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-21 16:04:11.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.275][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-09-21 16:04:11.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-09-21 16:04:11.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.280][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-09-21 16:04:11.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-09-21 16:04:11.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.285][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-09-21 16:04:11.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-09-21 16:04:11.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.299][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-21 16:04:11.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-21 16:04:11.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.304][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-21 16:04:11.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-21 16:04:11.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.309][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-21 16:04:11.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-21 16:04:11.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.314][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-21 16:04:11.315][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-21 16:04:11.316][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.317][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.318][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-21 16:04:11.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-21 16:04:11.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.339][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-09-21 16:04:11.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-09-21 16:04:11.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.344][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-09-21 16:04:11.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-09-21 16:04:11.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.349][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-09-21 16:04:11.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-09-21 16:04:11.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.354][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-09-21 16:04:11.355][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-09-21 16:04:11.356][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.357][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.359][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-09-21 16:04:11.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-09-21 16:04:11.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.373][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-09-21 16:04:11.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-09-21 16:04:11.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.378][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-09-21 16:04:11.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-09-21 16:04:11.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.383][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-09-21 16:04:11.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-09-21 16:04:11.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.388][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-09-21 16:04:11.389][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-09-21 16:04:11.390][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.392][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.393][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-09-21 16:04:11.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-09-21 16:04:11.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.408][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-21 16:04:11.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-21 16:04:11.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.413][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-21 16:04:11.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-21 16:04:11.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.417][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-21 16:04:11.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-21 16:04:11.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.422][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-21 16:04:11.423][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-21 16:04:11.425][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.426][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.427][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-21 16:04:11.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-21 16:04:11.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.442][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-21 16:04:11.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-21 16:04:11.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.448][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-21 16:04:11.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-21 16:04:11.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.455][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-21 16:04:11.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-21 16:04:11.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.462][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-21 16:04:11.464][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-21 16:04:11.466][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.468][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.469][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-21 16:04:11.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-21 16:04:11.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.484][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-21 16:04:11.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-21 16:04:11.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.489][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-21 16:04:11.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-21 16:04:11.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.494][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-21 16:04:11.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-21 16:04:11.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.499][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-21 16:04:11.500][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-21 16:04:11.501][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.503][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.504][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-21 16:04:11.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-21 16:04:11.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.523][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-21 16:04:11.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-21 16:04:11.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.528][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-21 16:04:11.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-21 16:04:11.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.533][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-21 16:04:11.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-21 16:04:11.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.538][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-21 16:04:11.539][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-21 16:04:11.540][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.542][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.543][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-21 16:04:11.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-21 16:04:11.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.557][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-09-21 16:04:11.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-09-21 16:04:11.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.562][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-09-21 16:04:11.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-09-21 16:04:11.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.567][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-09-21 16:04:11.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-09-21 16:04:11.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.572][ef$get] Asked field names are: description.
biodb.TRACE[2024-09-21 16:04:11.573][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-09-21 16:04:11.574][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.576][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.577][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-09-21 16:04:11.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-09-21 16:04:11.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.591][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-21 16:04:11.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-21 16:04:11.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.596][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-21 16:04:11.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-21 16:04:11.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.601][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-21 16:04:11.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-21 16:04:11.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.606][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-21 16:04:11.607][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-21 16:04:11.608][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.609][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.611][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-21 16:04:11.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-21 16:04:11.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.625][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-09-21 16:04:11.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-09-21 16:04:11.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.630][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-09-21 16:04:11.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-09-21 16:04:11.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.635][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-09-21 16:04:11.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-09-21 16:04:11.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.640][ef$get] Asked field names are: average.mass.
biodb.TRACE[2024-09-21 16:04:11.641][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-09-21 16:04:11.643][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.644][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.645][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-09-21 16:04:11.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-09-21 16:04:11.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.659][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-21 16:04:11.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-21 16:04:11.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.664][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-21 16:04:11.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-21 16:04:11.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.669][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-21 16:04:11.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-21 16:04:11.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.674][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-21 16:04:11.675][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-21 16:04:11.677][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.678][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.679][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-21 16:04:11.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-21 16:04:11.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.694][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-09-21 16:04:11.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-09-21 16:04:11.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.699][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-09-21 16:04:11.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-09-21 16:04:11.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.709][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-09-21 16:04:11.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-09-21 16:04:11.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.714][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-09-21 16:04:11.715][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-09-21 16:04:11.716][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.717][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.718][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-09-21 16:04:11.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-09-21 16:04:11.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.733][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-09-21 16:04:11.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-09-21 16:04:11.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.738][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-09-21 16:04:11.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-09-21 16:04:11.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.743][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-09-21 16:04:11.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-09-21 16:04:11.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.748][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-09-21 16:04:11.749][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-09-21 16:04:11.750][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.751][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.752][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-09-21 16:04:11.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-09-21 16:04:11.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.767][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-09-21 16:04:11.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-09-21 16:04:11.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.771][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-09-21 16:04:11.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-09-21 16:04:11.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.776][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-09-21 16:04:11.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-09-21 16:04:11.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.781][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-09-21 16:04:11.782][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-09-21 16:04:11.783][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.785][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.786][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-09-21 16:04:11.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-09-21 16:04:11.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.800][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-21 16:04:11.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-21 16:04:11.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.805][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-21 16:04:11.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-21 16:04:11.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.810][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-21 16:04:11.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-21 16:04:11.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.815][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-21 16:04:11.816][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-21 16:04:11.817][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.818][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.819][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-21 16:04:11.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-21 16:04:11.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.834][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-21 16:04:11.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-21 16:04:11.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.839][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-21 16:04:11.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-21 16:04:11.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.844][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-21 16:04:11.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-21 16:04:11.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.849][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-21 16:04:11.850][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-21 16:04:11.851][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.852][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.854][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-21 16:04:11.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-21 16:04:11.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.868][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-21 16:04:11.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-21 16:04:11.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.873][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-21 16:04:11.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-21 16:04:11.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.878][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-21 16:04:11.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-21 16:04:11.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.889][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-21 16:04:11.890][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-21 16:04:11.891][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.892][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.893][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-21 16:04:11.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-21 16:04:11.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.908][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-09-21 16:04:11.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-09-21 16:04:11.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.913][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-09-21 16:04:11.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-09-21 16:04:11.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.918][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-09-21 16:04:11.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-09-21 16:04:11.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.923][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-09-21 16:04:11.924][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-09-21 16:04:11.925][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.926][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.928][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-09-21 16:04:11.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-09-21 16:04:11.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.942][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-21 16:04:11.944][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-21 16:04:11.945][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.946][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.956][ef$get] Asked field names are: average.mass.
biodb.TRACE[2024-09-21 16:04:11.957][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-09-21 16:04:11.959][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.960][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.967][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-09-21 16:04:11.968][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-09-21 16:04:11.969][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.971][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.977][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-21 16:04:11.979][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-21 16:04:11.980][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.981][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.988][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-09-21 16:04:11.989][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-09-21 16:04:11.990][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:11.991][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:11.998][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-09-21 16:04:11.999][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-09-21 16:04:12.000][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:12.001][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:12.008][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-09-21 16:04:12.009][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-09-21 16:04:12.010][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:12.012][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:12.018][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-09-21 16:04:12.020][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-09-21 16:04:12.021][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:12.022][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:12.028][ef$get] Asked field names are: description.
biodb.TRACE[2024-09-21 16:04:12.030][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-09-21 16:04:12.031][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:12.032][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:12.039][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-21 16:04:12.040][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-21 16:04:12.041][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:12.043][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:12.049][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-21 16:04:12.051][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-21 16:04:12.052][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:12.053][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:12.060][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-21 16:04:12.061][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-21 16:04:12.062][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:12.063][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:12.070][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-21 16:04:12.071][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-21 16:04:12.072][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:12.073][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:12.080][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-21 16:04:12.081][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-21 16:04:12.083][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:12.084][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:12.096][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-21 16:04:12.097][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-21 16:04:12.098][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:12.099][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:12.106][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-21 16:04:12.107][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-21 16:04:12.109][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:12.110][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:12.116][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-09-21 16:04:12.118][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-09-21 16:04:12.119][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:12.120][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:04:12.127][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-21 16:04:12.128][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-21 16:04:12.129][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:12.130][ef$get] fields variable is a list.
biodb.INFO [2024-09-21 16:04:12.142][biodb::testThat]
biodb.INFO [2024-09-21 16:04:12.143][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-09-21 16:04:12.145][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-21 16:04:12.146][biodb::testThat]
biodb.DEBUG[2024-09-21 16:04:12.159][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2024-09-21 16:04:12.165][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.INFO [2024-09-21 16:04:12.171][self$getFolderPath] Create cache folder "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34" for "hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34".
biodb.DEBUG[2024-09-21 16:04:12.173][self$isDownloaded] Database hmdb.metabolites has not yet been downloaded.
biodb.INFO [2024-09-21 16:04:12.175][self$download] Downloading whole database of hmdb.metabolites.
biodb.INFO [2024-09-21 16:04:12.176][private$doDownload] Downloading HMDB metabolite database at "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip" ...
biodb.DEBUG[2024-09-21 16:04:12.179][sched$downloadFile] Downloading file "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
trying URL 'http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip'
biodb.INFO [2024-09-21 16:04:12.884][biodb::testThat]
biodb.INFO [2024-09-21 16:04:12.885][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-09-21 16:04:12.887][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-21 16:04:12.888][biodb::testThat]
biodb.TRACE[2024-09-21 16:04:12.891][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-21 16:04:12.893][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-21 16:04:12.894][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:04:12.895][ef$get] fields variable is a list.
biodb.DEBUG[2024-09-21 16:04:12.897][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "name".
biodb.DEBUG[2024-09-21 16:04:12.928][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2024-09-21 16:04:12.968][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2024-09-21 16:04:12.970][self$isDownloaded] Database hmdb.metabolites has not yet been downloaded.
biodb.INFO [2024-09-21 16:04:12.971][self$download] Downloading whole database of hmdb.metabolites.
biodb.INFO [2024-09-21 16:04:12.973][private$doDownload] Downloading HMDB metabolite database at "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip" ...
biodb.DEBUG[2024-09-21 16:04:12.987][sched$downloadFile] Downloading file "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
trying URL 'http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip'
biodb.INFO [2024-09-21 16:04:13.504][biodb::testThat]
biodb.INFO [2024-09-21 16:04:13.505][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-09-21 16:04:13.507][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-21 16:04:13.508][biodb::testThat]
biodb.DEBUG[2024-09-21 16:04:13.518][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2024-09-21 16:04:13.519][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2024-09-21 16:04:13.521][self$isDownloaded] Database hmdb.metabolites has not yet been downloaded.
biodb.INFO [2024-09-21 16:04:13.522][self$download] Downloading whole database of hmdb.metabolites.
biodb.INFO [2024-09-21 16:04:13.524][private$doDownload] Downloading HMDB metabolite database at "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip" ...
biodb.DEBUG[2024-09-21 16:04:13.526][sched$downloadFile] Downloading file "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
trying URL 'http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip'
Content type 'application/zip' length 953913010 bytes (909.7 MB)
=======
downloaded 141.4 MB

biodb.INFO [2024-09-21 16:06:52.332][biodb::testThat]
biodb.INFO [2024-09-21 16:06:52.334][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-09-21 16:06:52.335][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-21 16:06:52.336][biodb::testThat]
biodb.DEBUG[2024-09-21 16:06:52.342][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2024-09-21 16:06:52.343][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2024-09-21 16:06:52.345][self$isDownloaded] Database hmdb.metabolites has not yet been downloaded.
biodb.INFO [2024-09-21 16:06:52.346][self$download] Downloading whole database of hmdb.metabolites.
biodb.INFO [2024-09-21 16:06:52.348][private$doDownload] Downloading HMDB metabolite database at "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip" ...
biodb.DEBUG[2024-09-21 16:06:52.351][sched$downloadFile] Downloading file "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
trying URL 'http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip'
Content type 'application/zip' length 953913010 bytes (909.7 MB)
==================================================
downloaded 909.7 MB

biodb.TRACE[2024-09-21 16:10:44.430][cch$addFilesToCache] Moving files to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/tmp\hmdb.metabolites20bb450a41b56zip".
biodb.TRACE[2024-09-21 16:10:44.433][private$doAddFilesToCache] Destination files are [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip".
biodb.DEBUG[2024-09-21 16:10:44.440][cch$addFilesToCache] Done adding files.
biodb.DEBUG[2024-09-21 16:10:44.442][self$getDownloadPath] Download path of hmdb.metabolites is "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip".
biodb.DEBUG[2024-09-21 16:10:44.444][self$download] Downloading of hmdb.metabolites completed.
biodb.TRACE[2024-09-21 16:10:44.448][self$addFilesToCache] Moving files to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/tmp\marker20bb451632684marker".
biodb.TRACE[2024-09-21 16:10:44.449][private$doAddFilesToCache] Destination files are [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/downloaded.marker".
biodb.DEBUG[2024-09-21 16:10:44.454][self$addFilesToCache] Done adding files.
biodb.DEBUG[2024-09-21 16:10:44.456][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.INFO [2024-09-21 16:10:44.458][self$download] Extract whole database of hmdb.metabolites.
biodb.INFO [2024-09-21 16:10:44.460][private$doExtractDownload] Extracting content of downloaded',
                    ' HMDB metabolite database...
biodb.DEBUG[2024-09-21 16:10:44.462][self$getDownloadPath] Download path of hmdb.metabolites is "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip".
biodb.DEBUG[2024-09-21 16:10:44.463][private$doExtractDownload] Unzipping C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip into C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/tmp...
biodb.DEBUG[2024-09-21 16:11:18.395][private$findXmlDatabaseFile] Found files [2]: "hmdb.metabolites20bb451307f7bzip, hmdb_metabolites.xml" into C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/download.zip.
biodb.DEBUG[2024-09-21 16:11:18.397][private$findXmlDatabaseFile] Found XML file C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/tmp/hmdb_metabolites.xml in ZIP file.
biodb.DEBUG[2024-09-21 16:11:18.399][private$doExtractDownload] Delete existing entry files in cache system.
biodb.DEBUG[2024-09-21 16:11:18.401][private$doExtractDownload] Extract entries from XML file "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/tmp/hmdb_metabolites.xml", into "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/tmp".
biodb.TRACE[2024-09-21 16:37:48.777][self$addFilesToCache] Moving files to cache [217920]: "C:\Users\biocbuild\AppData\Local\R\cache\R\biodb\tmp/HMDB0000001.xml, C:\Users\biocbuild\AppData\Local\R\cache\R\biodb\tmp/HMDB0000002.xml, C:\Users\biocbuild\AppData\Local\R\cache\R\biodb\tmp/HMDB0000005.xml, C:\Users\biocbuild\AppData\Local\R\cache\R\biodb\tmp/HMDB0000008.xml, C:\Users\biocbuild\AppData\Local\R\cache\R\biodb\tmp/HMDB0000010.xml, C:\Users\biocbuild\AppData\Local\R\cache\R\biodb\tmp/HMDB0000011.xml, C:\Users\biocbuild\AppData\Local\R\cache\R\biodb\tmp/HMDB0000012.xml, C:\Users\biocbuild\AppData\Local\R\cache\R\biodb\tmp/HMDB0000014.xml, C:\Users\biocbuild\AppData\Local\R\cache\R\biodb\tmp/HMDB0000015.xml, C:\Users\biocbuild\AppData\Local\R\cache\R\biodb\tmp/HMDB0000016.xml, ...".
biodb.TRACE[2024-09-21 16:37:49.806][private$doAddFilesToCache] Destination files are [217920]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000001.xml, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000002.xml, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000005.xml, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000008.xml, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000010.xml, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000011.xml, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000012.xml, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000014.xml, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000015.xml, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000016.xml, ...".
biodb.DEBUG[2024-09-21 16:52:24.144][self$addFilesToCache] Done adding files.
biodb.DEBUG[2024-09-21 16:52:24.146][private$doExtractDownload] Delete extracted database.
biodb.TRACE[2024-09-21 16:52:24.383][self$addFilesToCache] Moving files to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/tmp\marker20bb454384b04marker".
biodb.TRACE[2024-09-21 16:52:24.384][private$doAddFilesToCache] Destination files are [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/extracted.marker".
biodb.DEBUG[2024-09-21 16:52:24.390][self$addFilesToCache] Done adding files.
biodb.TRACE[2024-09-21 16:52:24.392][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000001".
biodb.TRACE[2024-09-21 16:52:24.394][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-09-21 16:52:24.414][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000001.xml".
biodb.DEBUG[2024-09-21 16:52:24.415][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2024-09-21 16:52:24.441][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2024-09-21 16:52:24.442][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2024-09-21 16:52:24.445][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-09-21 16:52:24.446][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-21 16:52:24.447][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-21 16:52:24.455][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-09-21 16:52:24.456][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-21 16:52:24.458][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:52:24.459][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-09-21 16:52:24.465][ef$get] Asked field names are: accession.
biodb.TRACE[2024-09-21 16:52:24.467][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-21 16:52:24.468][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:24.469][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:24.470][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-21 16:52:24.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-21 16:52:24.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:24.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:24.475][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-09-21 16:52:24.477][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-09-21 16:52:24.478][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:24.479][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:24.481][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-09-21 16:52:24.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-09-21 16:52:24.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:24.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:24.486][ef$get] Asked field names are: average.mass.
biodb.TRACE[2024-09-21 16:52:24.487][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-09-21 16:52:24.488][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:24.489][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:24.491][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-09-21 16:52:24.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-09-21 16:52:24.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:24.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:24.496][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-09-21 16:52:24.498][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-09-21 16:52:24.499][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:24.500][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:24.501][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-09-21 16:52:24.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-09-21 16:52:24.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:24.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:24.506][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-21 16:52:24.508][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-21 16:52:24.509][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:24.510][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:24.511][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-21 16:52:24.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-21 16:52:24.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:24.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:24.517][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-09-21 16:52:24.518][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-09-21 16:52:24.519][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:24.521][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:24.522][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-09-21 16:52:24.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-09-21 16:52:24.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:24.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:24.527][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-21 16:52:24.528][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-21 16:52:24.530][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:24.531][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:24.533][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-21 16:52:24.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-21 16:52:24.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:24.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:24.538][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-21 16:52:24.539][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-21 16:52:24.541][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:24.542][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:24.543][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-21 16:52:24.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-21 16:52:24.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:24.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:24.549][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-09-21 16:52:24.550][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-09-21 16:52:24.552][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:24.553][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:24.554][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-09-21 16:52:24.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-09-21 16:52:24.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:24.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:24.560][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-09-21 16:52:24.561][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-09-21 16:52:24.563][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:24.564][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:24.566][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-09-21 16:52:24.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-09-21 16:52:24.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:24.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:24.572][ef$get] Asked field names are: formula.
biodb.TRACE[2024-09-21 16:52:24.573][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-21 16:52:24.575][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:24.576][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:24.578][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-21 16:52:24.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-21 16:52:24.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:24.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:24.583][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-09-21 16:52:24.585][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-21 16:52:24.586][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:24.587][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:24.589][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-21 16:52:24.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-21 16:52:24.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:24.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:24.595][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-21 16:52:24.596][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-21 16:52:24.597][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:24.599][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:24.601][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-21 16:52:24.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-21 16:52:24.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:24.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:24.606][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-21 16:52:24.608][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-21 16:52:24.609][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:24.610][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:24.612][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-21 16:52:24.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-21 16:52:24.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:24.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:24.618][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-21 16:52:24.619][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-21 16:52:24.621][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:24.622][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:24.624][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-21 16:52:24.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-21 16:52:24.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:24.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:24.629][ef$get] Asked field names are: description.
biodb.TRACE[2024-09-21 16:52:24.631][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-09-21 16:52:24.632][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:24.633][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:24.635][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-09-21 16:52:24.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-09-21 16:52:24.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:24.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:24.641][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-09-21 16:52:24.642][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-21 16:52:24.643][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:24.645][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:24.647][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-21 16:52:24.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-21 16:52:24.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:24.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:24.652][ef$get] Asked field names are: super.class.
biodb.TRACE[2024-09-21 16:52:24.654][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-09-21 16:52:24.655][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:24.656][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:24.658][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2024-09-21 16:52:24.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-09-21 16:52:24.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:24.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:24.664][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-21 16:52:24.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-21 16:52:24.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:24.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:24.670][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-21 16:52:24.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-21 16:52:24.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:24.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:24.675][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-21 16:52:24.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-21 16:52:24.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:24.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:24.680][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-09-21 16:52:24.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-09-21 16:52:24.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:24.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:24.686][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-09-21 16:52:24.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-09-21 16:52:24.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:24.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:24.691][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-09-21 16:52:24.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-09-21 16:52:24.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:24.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:24.697][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-09-21 16:52:24.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-09-21 16:52:24.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:24.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:24.702][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-09-21 16:52:24.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-09-21 16:52:24.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:24.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:24.707][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-09-21 16:52:24.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-09-21 16:52:24.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:24.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:24.713][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-21 16:52:24.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-21 16:52:24.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:24.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:24.718][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-21 16:52:24.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-21 16:52:24.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:24.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:24.724][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-09-21 16:52:24.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-09-21 16:52:24.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:24.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:24.730][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-09-21 16:52:24.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-09-21 16:52:24.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:24.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:24.735][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-09-21 16:52:24.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-09-21 16:52:24.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:24.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:24.741][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-09-21 16:52:24.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-09-21 16:52:24.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:24.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:24.746][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-09-21 16:52:24.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-09-21 16:52:24.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:24.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:24.752][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-09-21 16:52:24.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-09-21 16:52:24.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:24.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:24.758][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-09-21 16:52:24.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-09-21 16:52:24.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:24.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:24.764][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-09-21 16:52:24.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-09-21 16:52:24.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:24.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:24.770][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-09-21 16:52:24.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-09-21 16:52:24.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:24.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:24.775][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-09-21 16:52:24.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-09-21 16:52:24.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:24.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:24.781][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-09-21 16:52:24.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-09-21 16:52:24.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:24.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:24.786][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-09-21 16:52:24.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-09-21 16:52:24.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:24.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:24.791][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-09-21 16:52:24.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-09-21 16:52:24.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:24.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:24.797][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-09-21 16:52:24.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-09-21 16:52:24.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:24.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:24.802][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-09-21 16:52:24.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-09-21 16:52:24.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:24.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:24.808][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-09-21 16:52:24.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-09-21 16:52:24.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:24.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:24.813][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-21 16:52:24.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-21 16:52:24.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:24.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:24.819][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-21 16:52:24.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-21 16:52:24.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:24.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:24.824][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-09-21 16:52:24.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-09-21 16:52:24.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:24.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:24.830][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-21 16:52:24.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-21 16:52:24.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:24.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:24.835][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-21 16:52:24.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-21 16:52:24.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:24.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:24.840][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-09-21 16:52:24.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-09-21 16:52:24.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:24.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:24.846][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-21 16:52:24.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-21 16:52:24.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:24.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:24.851][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-21 16:52:24.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-21 16:52:24.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:24.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:24.856][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-21 16:52:24.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-21 16:52:24.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:24.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:24.862][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-21 16:52:24.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-21 16:52:24.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:24.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:24.867][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-21 16:52:24.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-21 16:52:24.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:24.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:24.873][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-09-21 16:52:24.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-09-21 16:52:24.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:24.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:24.878][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-21 16:52:24.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-21 16:52:24.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:24.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:24.884][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-21 16:52:24.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-21 16:52:24.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:24.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:24.889][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-09-21 16:52:24.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-09-21 16:52:24.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:24.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:24.894][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-21 16:52:24.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-21 16:52:24.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:24.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:24.901][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-21 16:52:24.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-21 16:52:24.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:24.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:24.963][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-21 16:52:24.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-21 16:52:24.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:24.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:24.967][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-21 16:52:24.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-21 16:52:24.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:24.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:24.972][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-21 16:52:24.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-21 16:52:24.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:24.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:24.977][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-21 16:52:24.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-09-21 16:52:24.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:24.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:24.982][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-09-21 16:52:24.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-09-21 16:52:24.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:24.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:24.986][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-09-21 16:52:24.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-09-21 16:52:24.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:24.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:24.991][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-09-21 16:52:24.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-09-21 16:52:24.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:24.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:24.996][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-21 16:52:24.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-21 16:52:24.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:24.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:25.000][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-21 16:52:25.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-21 16:52:25.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:25.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:25.005][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-09-21 16:52:25.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-09-21 16:52:25.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:25.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:25.010][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2024-09-21 16:52:25.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-21 16:52:25.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:25.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:25.015][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-21 16:52:25.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-21 16:52:25.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:25.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:25.019][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-21 16:52:25.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-21 16:52:25.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:25.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:25.024][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-09-21 16:52:25.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-21 16:52:25.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:25.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:25.029][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2024-09-21 16:52:25.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-09-21 16:52:25.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:25.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:25.034][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-21 16:52:25.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-21 16:52:25.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:25.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:25.039][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-21 16:52:25.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-21 16:52:25.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:25.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:25.044][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-21 16:52:25.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-21 16:52:25.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:25.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:25.048][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-21 16:52:25.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-21 16:52:25.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:25.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:25.053][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-09-21 16:52:25.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-09-21 16:52:25.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:25.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:25.058][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-09-21 16:52:25.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-09-21 16:52:25.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:25.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:25.063][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-09-21 16:52:25.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-09-21 16:52:25.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:25.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:25.067][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-21 16:52:25.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-21 16:52:25.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:25.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:25.072][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-09-21 16:52:25.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-09-21 16:52:25.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:25.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:25.077][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-21 16:52:25.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-21 16:52:25.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:25.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:25.081][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-21 16:52:25.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-21 16:52:25.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:25.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:25.086][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-21 16:52:25.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-21 16:52:25.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:25.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:25.091][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-21 16:52:25.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-21 16:52:25.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:25.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:25.096][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-21 16:52:25.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-21 16:52:25.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:25.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:25.101][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-09-21 16:52:25.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-09-21 16:52:25.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:25.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-09-21 16:52:25.105][self$createEntryFromContent] Accession numbers: HMDB0000001.
biodb.TRACE[2024-09-21 16:52:25.125][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-09-21 16:52:25.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-09-21 16:52:25.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:25.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:25.130][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-09-21 16:52:25.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-09-21 16:52:25.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:25.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:25.135][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-09-21 16:52:25.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-09-21 16:52:25.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:25.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:25.140][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-09-21 16:52:25.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-09-21 16:52:25.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:25.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:25.178][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-09-21 16:52:25.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-09-21 16:52:25.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:25.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:25.183][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-09-21 16:52:25.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-09-21 16:52:25.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:25.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:25.188][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-09-21 16:52:25.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-09-21 16:52:25.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:25.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:52:25.193][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-09-21 16:52:25.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-09-21 16:52:25.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:52:25.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-09-21 16:52:25.207][biodb::testThat]
biodb.INFO [2024-09-21 16:52:25.209][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-09-21 16:52:25.210][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-21 16:52:25.211][biodb::testThat]
biodb.INFO [2024-09-21 16:52:25.223][biodb::testThat]
biodb.INFO [2024-09-21 16:52:25.224][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-09-21 16:52:25.225][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-21 16:52:25.226][biodb::testThat]
biodb.INFO [2024-09-21 16:52:25.237][biodb::testThat]
biodb.INFO [2024-09-21 16:52:25.238][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-09-21 16:52:25.240][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-21 16:52:25.241][biodb::testThat]
biodb.DEBUG[2024-09-21 16:52:25.246][function(conn, opt)] Trying to download "http://www.hmdb.ca/metabolites/HMDB0000001".
biodb.DEBUG[2024-09-21 16:52:26.035][getUrlContent] Use base::url() for downloading content of URL http://www.hmdb.ca/metabolites/HMDB0000001.
biodb.INFO [2024-09-21 16:52:54.258][biodb::testThat]
biodb.INFO [2024-09-21 16:52:54.259][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-09-21 16:52:54.260][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-09-21 16:52:54.262][biodb::testThat]
biodb.DEBUG[2024-09-21 16:52:54.490][getUrlContent] Use base::url() for downloading content of URL http://www.hmdb.ca/structures/HMDB0000001/image.png.
biodb.TRACE[2024-09-21 16:53:16.466][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-21 16:53:16.467][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-21 16:53:16.468][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:53:16.470][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:53:16.471][ef$get] Asked field names are: description.
biodb.TRACE[2024-09-21 16:53:16.472][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-09-21 16:53:16.473][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:53:16.474][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:53:16.476][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-09-21 16:53:16.477][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-09-21 16:53:16.478][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:53:16.479][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:53:16.480][ef$get] Asked field names are: name.
biodb.TRACE[2024-09-21 16:53:16.482][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-09-21 16:53:16.483][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:53:16.484][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:53:16.485][ef$get] Asked field names are: description.
biodb.TRACE[2024-09-21 16:53:16.486][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-09-21 16:53:16.488][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:53:16.489][ef$get] fields variable is a list.
biodb.TRACE[2024-09-21 16:53:16.490][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-09-21 16:53:16.491][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-09-21 16:53:16.492][ef$get] 1 fields were returned.
biodb.TRACE[2024-09-21 16:53:16.494][ef$get] fields variable is a list.
biodb.INFO [2024-09-21 16:53:16.495][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-09-21 16:53:16.496][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler
biodb.INFO [2024-09-21 16:53:16.498][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2024-09-21 16:53:16.499][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-09-21 16:53:16.500][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-09-21 16:53:16.501][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-09-21 16:53:16.502][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-09-21 16:53:16.503][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-09-21 16:53:16.504][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-09-21 16:53:16.505][FUN] Functions in observer 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 3 | WARN 6 | SKIP 0 | PASS 117 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_long_100_generic.R:42:1'): RT unit is defined when there is an RT value. ──
Error in `utils::download.file(url = url, destfile = dest.file, mode = "wb", 
    method = "auto", cacheOK = FALSE, quiet = FALSE)`: cannot open URL 'http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip'
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
 3.   └─conn$getBiodb()$getFactory()$getEntry(...)
 4.     └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
 5.       └─conn$getEntryContent(ids)
 6.         └─self$download()
 7.           └─private$doDownload()
 8.             └─sched$downloadFile(url = zip.url, dest.file = tmpFile)
 9.               └─utils::download.file(...)
── Error ('test_long_100_generic.R:42:1'): We can search for an entry by searchable field ──
Error in `utils::download.file(url = url, destfile = dest.file, mode = "wb", 
    method = "auto", cacheOK = FALSE, quiet = FALSE)`: cannot open URL 'http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip'
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
  3.   └─conn$getEntry(id, drop = TRUE)
  4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
  5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  6.         └─conn$getEntryContent(ids)
  7.           └─self$download()
  8.             └─private$doDownload()
  9.               └─sched$downloadFile(url = zip.url, dest.file = tmpFile)
 10.                 └─utils::download.file(...)
── Error ('test_long_100_generic.R:42:1'): We can search for an entry by name. ──
Error in `utils::download.file(url = url, destfile = dest.file, mode = "wb", 
    method = "auto", cacheOK = FALSE, quiet = FALSE)`: download from 'http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip' failed
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
  3.   └─conn$getEntry(id, drop = TRUE)
  4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
  5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  6.         └─conn$getEntryContent(ids)
  7.           └─self$download()
  8.             └─private$doDownload()
  9.               └─sched$downloadFile(url = zip.url, dest.file = tmpFile)
 10.                 └─utils::download.file(...)

[ FAIL 3 | WARN 6 | SKIP 0 | PASS 117 ]
Error: Test failures
Execution halted

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbHmdb_1.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc-longtests/meat/biodbHmdb.Rcheck'
* using R version 4.4.1 (2024-06-14 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using options '--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error'
* checking for file 'biodbHmdb/DESCRIPTION' ... OK
* this is package 'biodbHmdb' version '1.11.0'
* 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 whether package 'biodbHmdb' can be installed ... WARNING
Found the following significant warnings:
  EntryMaker.hpp:23:21: warning: 'EntryMaker::accession_tag' will be initialized after [-Wreorder]
  EntryMaker.hpp:22:14: warning:   'bool EntryMaker::closed' [-Wreorder]
  EntryMaker.cpp:5:1: warning:   when initialized here [-Wreorder]
See 'F:/biocbuild/bbs-3.20-bioc-longtests/meat/biodbHmdb.Rcheck/00install.out' for details.
* used C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
* 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 ... NOTE
Namespace in Imports field not imported from: 'zip'
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  'HmdbMetabolitesConn' 'HmdbMetabolitesEntry' 'hmdbToSqlite'
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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'
 ERROR
Running the tests in 'longtests/testthat.R' failed.
Last 13 lines of output:
       ▆
    1. ├─base::do.call(fct, params)
    2. └─biodb (local) `<fn>`(conn = `<HmdbMtbC>`, opt = `<named list>`)
    3.   └─conn$getEntry(id, drop = TRUE)
    4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
    5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
    6.         └─conn$getEntryContent(ids)
    7.           └─self$download()
    8.             └─private$doDownload()
    9.               └─sched$downloadFile(url = zip.url, dest.file = tmpFile)
   10.                 └─utils::download.file(...)
  
  [ FAIL 3 | WARN 6 | SKIP 0 | PASS 117 ]
  Error: Test failures
  Execution halted
* DONE

Status: 1 ERROR, 2 WARNINGs, 1 NOTE
See
  'F:/biocbuild/bbs-3.20-bioc-longtests/meat/biodbHmdb.Rcheck/00check.log'
for details.

Installation output

biodbHmdb.Rcheck/00install.out

* installing *source* package 'biodbHmdb' ...
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/testthat/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c EntryMaker.cpp -o EntryMaker.o
In file included from EntryMaker.cpp:1:
EntryMaker.hpp: In constructor 'EntryMaker::EntryMaker()':
EntryMaker.hpp:23:21: warning: 'EntryMaker::accession_tag' will be initialized after [-Wreorder]
   23 |         TagDetector accession_tag;
      |                     ^~~~~~~~~~~~~
EntryMaker.hpp:22:14: warning:   'bool EntryMaker::closed' [-Wreorder]
   22 |         bool closed;
      |              ^~~~~~
EntryMaker.cpp:5:1: warning:   when initialized here [-Wreorder]
    5 | EntryMaker::EntryMaker() :
      | ^~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/testthat/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c FileEntryMaker.cpp -o FileEntryMaker.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/testthat/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/testthat/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c StringEnrtryMaker.cpp -o StringEnrtryMaker.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/testthat/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c TagDetector.cpp -o TagDetector.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/testthat/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c XmlSplitter.cpp -o XmlSplitter.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/testthat/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c extractXmlEntries.cpp -o extractXmlEntries.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/testthat/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c test-100-TagDetector.cpp -o test-100-TagDetector.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/testthat/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c test-150-StringEntryMaker.cpp -o test-150-StringEntryMaker.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/testthat/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c test-200-XmlSplitter.cpp -o test-200-XmlSplitter.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/testthat/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c test-runner.cpp -o test-runner.o
g++ -std=gnu++17 -shared -s -static-libgcc -o biodbHmdb.dll tmp.def EntryMaker.o FileEntryMaker.o RcppExports.o StringEnrtryMaker.o TagDetector.o XmlSplitter.o extractXmlEntries.o test-100-TagDetector.o test-150-StringEntryMaker.o test-200-XmlSplitter.o test-runner.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.20-bioc-longtests/meat/biodbHmdb.Rcheck/00LOCK-biodbHmdb/00new/biodbHmdb/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
** help
No man pages found in package  'biodbHmdb' 
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (biodbHmdb)