| Back to Long Tests report for BioC 3.18 |
This page was generated on 2024-04-13 23:55:02 -0400 (Sat, 13 Apr 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4675 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4413 |
| merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4436 |
| 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 8/30 | Hostname | OS / Arch | CHECK | |||||||
| biodbHmdb 1.8.0 (landing page) Pierrick Roger
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | WARNINGS | |||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | WARNINGS | ||||||||
| merida1 | macOS 12.7.1 Monterey / x86_64 | WARNINGS | ||||||||
|
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. |
| Package: biodbHmdb |
| Version: 1.8.0 |
| Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbHmdb_1.8.0.tar.gz |
| StartedAt: 2024-04-13 16:04:43 -0400 (Sat, 13 Apr 2024) |
| EndedAt: 2024-04-13 16:05:58 -0400 (Sat, 13 Apr 2024) |
| EllapsedTime: 74.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: biodbHmdb.Rcheck |
| Warnings: 2 |
biodbHmdb.Rcheck/tests/testthat.Rout
R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # 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 [2024-04-13 16:05:51.757][biodb::testContext]
biodb.INFO [2024-04-13 16:05:51.759][biodb::testContext] ********************************************************************************
biodb.INFO [2024-04-13 16:05:51.760][biodb::testContext] Test context - Generic long tests
biodb.INFO [2024-04-13 16:05:51.761][biodb::testContext] ********************************************************************************
biodb.INFO [2024-04-13 16:05:51.762][biodb::testContext]
biodb.INFO [2024-04-13 16:05:51.769][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.10.0.
biodb.DEBUG[2024-04-13 16:05:51.771][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.18-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-04-13 16:05:51.779][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-04-13 16:05:51.780][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-04-13 16:05:51.781][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-04-13 16:05:51.782][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:51.783][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:51.784][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:51.785][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-04-13 16:05:51.804][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-04-13 16:05:51.805][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:51.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:51.807][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:51.808][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-04-13 16:05:51.809][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-04-13 16:05:51.810][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:51.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:51.812][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:51.813][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-04-13 16:05:51.814][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-04-13 16:05:51.815][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-04-13 16:05:51.816][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:51.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:51.818][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:51.819][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-04-13 16:05:51.820][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-04-13 16:05:51.821][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-04-13 16:05:51.822][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:51.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:51.824][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:51.825][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-04-13 16:05:51.826][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-04-13 16:05:51.826][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:51.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:51.828][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:51.839][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-04-13 16:05:51.840][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-04-13 16:05:51.841][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-04-13 16:05:51.842][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:51.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:51.843][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:51.844][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-04-13 16:05:51.845][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-04-13 16:05:51.846][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:51.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:51.847][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:51.848][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-04-13 16:05:51.849][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-04-13 16:05:51.850][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-04-13 16:05:51.851][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:51.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:51.852][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:51.853][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-04-13 16:05:51.854][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-04-13 16:05:51.855][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-04-13 16:05:51.856][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-04-13 16:05:51.857][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-04-13 16:05:51.858][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-04-13 16:05:51.858][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:51.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:51.860][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:51.861][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-04-13 16:05:51.862][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-04-13 16:05:51.863][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:51.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:51.864][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:51.865][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-04-13 16:05:51.866][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-04-13 16:05:51.867][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:51.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:51.868][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:51.869][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-04-13 16:05:51.870][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-04-13 16:05:51.871][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:51.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:51.873][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:51.873][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-04-13 16:05:51.874][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-04-13 16:05:51.875][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:51.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:51.877][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:51.878][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-04-13 16:05:51.879][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-04-13 16:05:51.880][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:51.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:51.881][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:51.882][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-04-13 16:05:51.883][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-04-13 16:05:51.886][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-04-13 16:05:51.887][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:51.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:51.889][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:51.889][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-04-13 16:05:51.890][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-04-13 16:05:51.891][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-04-13 16:05:51.892][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:51.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:51.894][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:51.897][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-04-13 16:05:51.928][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-04-13 16:05:51.942][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-04-13 16:05:51.943][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:51.944][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-13 16:05:51.945][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:51.946][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-13 16:05:51.947][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-13 16:05:51.948][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-13 16:05:51.949][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-04-13 16:05:51.950][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-13 16:05:51.951][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:51.952][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-04-13 16:05:51.953][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-13 16:05:51.953][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:05:51.954][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:51.955][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-04-13 16:05:51.955][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-04-13 16:05:51.955][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-04-13 16:05:51.955][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-04-13 16:05:51.955][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-04-13 16:05:51.956][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-13 16:05:51.957][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-13 16:05:51.958][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-13 16:05:51.959][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-13 16:05:51.960][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-13 16:05:51.961][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-13 16:05:51.961][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-13 16:05:51.962][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:05:51.963][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-13 16:05:51.964][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-13 16:05:51.965][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-13 16:05:51.966][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:05:51.967][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-04-13 16:05:51.969][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-04-13 16:05:51.969][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-04-13 16:05:51.970][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:51.971][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-13 16:05:51.972][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:51.973][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-13 16:05:51.974][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-13 16:05:51.975][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-13 16:05:51.976][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-04-13 16:05:51.977][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-13 16:05:51.978][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:51.978][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-04-13 16:05:51.979][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-13 16:05:51.980][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:05:51.981][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:51.982][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-04-13 16:05:51.982][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-04-13 16:05:51.982][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-04-13 16:05:51.982][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-04-13 16:05:51.982][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-04-13 16:05:51.983][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-13 16:05:51.984][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-13 16:05:51.985][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-13 16:05:51.986][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-13 16:05:51.986][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-13 16:05:51.987][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-13 16:05:51.988][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-13 16:05:51.989][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:05:51.990][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-13 16:05:51.991][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-13 16:05:51.992][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-13 16:05:51.992][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:05:51.993][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-04-13 16:05:51.995][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:51.996][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-04-13 16:05:51.997][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:51.998][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-13 16:05:51.999][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:52.000][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-13 16:05:52.001][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-13 16:05:52.001][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-13 16:05:52.002][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-04-13 16:05:52.003][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-13 16:05:52.004][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-04-13 16:05:52.005][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-04-13 16:05:52.006][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-13 16:05:52.007][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:05:52.008][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:52.009][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:05:52.009][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-13 16:05:52.010][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-13 16:05:52.011][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-13 16:05:52.012][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-13 16:05:52.013][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-13 16:05:52.014][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-13 16:05:52.015][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-13 16:05:52.015][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:05:52.016][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-13 16:05:52.017][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-13 16:05:52.018][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-13 16:05:52.019][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:05:52.024][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-04-13 16:05:52.026][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:52.027][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-04-13 16:05:52.028][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:52.029][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-13 16:05:52.030][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:52.030][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-13 16:05:52.031][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-13 16:05:52.032][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-13 16:05:52.033][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-04-13 16:05:52.034][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-13 16:05:52.035][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-04-13 16:05:52.036][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-04-13 16:05:52.037][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-13 16:05:52.038][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:05:52.038][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:52.039][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:05:52.040][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-13 16:05:52.041][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-13 16:05:52.042][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-13 16:05:52.043][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-13 16:05:52.044][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-13 16:05:52.044][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-13 16:05:52.045][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-13 16:05:52.046][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:05:52.047][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-13 16:05:52.048][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-13 16:05:52.049][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-13 16:05:52.049][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:05:52.053][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-04-13 16:05:52.054][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:52.055][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:52.056][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:52.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:52.057][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:52.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:52.059][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:52.060][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:52.061][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:52.061][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:52.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:52.063][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:52.064][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:52.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:52.065][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:52.066][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:52.067][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:52.068][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:52.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:52.069][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:52.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:52.071][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:52.072][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:52.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:52.073][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:52.074][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:52.075][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:52.076][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:52.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:52.077][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:52.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:52.079][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:52.080][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:52.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:52.082][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:52.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:52.083][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:52.084][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:52.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:52.085][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:52.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:52.087][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:52.088][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:52.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:52.090][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:52.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:52.091][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:52.092][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:52.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:52.094][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:52.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:52.095][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:52.096][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:52.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:52.098][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:52.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:52.099][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:52.100][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:52.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:52.102][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:52.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:52.103][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:52.104][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:52.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:52.106][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:52.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:52.107][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:52.108][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:52.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:52.110][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:52.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:52.111][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:52.112][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:52.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:52.114][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:52.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:52.115][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:52.116][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:52.117][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:52.118][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:52.123][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:52.124][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:52.125][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:52.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:52.127][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:52.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:52.128][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:52.130][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-04-13 16:05:52.136][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-04-13 16:05:52.137][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-04-13 16:05:52.138][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-04-13 16:05:52.140][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-04-13 16:05:52.141][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-04-13 16:05:52.143][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-04-13 16:05:52.144][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-04-13 16:05:52.146][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-04-13 16:05:52.147][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-04-13 16:05:52.148][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-04-13 16:05:52.150][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-04-13 16:05:52.151][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-04-13 16:05:52.152][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-04-13 16:05:52.154][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-04-13 16:05:52.155][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-04-13 16:05:52.157][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-04-13 16:05:52.158][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-04-13 16:05:52.159][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-04-13 16:05:52.161][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-04-13 16:05:52.162][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-04-13 16:05:52.164][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-04-13 16:05:52.165][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-04-13 16:05:52.166][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-04-13 16:05:52.168][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-04-13 16:05:52.169][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-04-13 16:05:52.171][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-04-13 16:05:52.172][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-04-13 16:05:52.173][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-04-13 16:05:52.175][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-04-13 16:05:52.176][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-04-13 16:05:52.178][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-04-13 16:05:52.179][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-04-13 16:05:52.180][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-04-13 16:05:52.182][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-04-13 16:05:52.183][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-04-13 16:05:52.184][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-04-13 16:05:52.186][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-04-13 16:05:52.187][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-04-13 16:05:52.189][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-04-13 16:05:52.190][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-04-13 16:05:52.191][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-04-13 16:05:52.193][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-04-13 16:05:52.194][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-04-13 16:05:52.195][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-04-13 16:05:52.197][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-04-13 16:05:52.198][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-04-13 16:05:52.200][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-04-13 16:05:52.201][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-04-13 16:05:52.202][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-04-13 16:05:52.204][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-04-13 16:05:52.205][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-04-13 16:05:52.207][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-04-13 16:05:52.208][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-04-13 16:05:52.209][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-04-13 16:05:52.211][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-04-13 16:05:52.212][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-04-13 16:05:52.214][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-04-13 16:05:52.215][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-04-13 16:05:52.216][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-04-13 16:05:52.218][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-04-13 16:05:52.233][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-04-13 16:05:52.234][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-04-13 16:05:52.235][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-04-13 16:05:52.237][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-04-13 16:05:52.238][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-04-13 16:05:52.239][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-04-13 16:05:52.241][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-04-13 16:05:52.242][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-04-13 16:05:52.243][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-04-13 16:05:52.244][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-04-13 16:05:52.246][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-04-13 16:05:52.247][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-04-13 16:05:52.249][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-04-13 16:05:52.250][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-04-13 16:05:52.251][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-04-13 16:05:52.253][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-04-13 16:05:52.254][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-04-13 16:05:52.256][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-04-13 16:05:52.257][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-04-13 16:05:52.258][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-04-13 16:05:52.260][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-04-13 16:05:52.261][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-04-13 16:05:52.267][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-04-13 16:05:52.269][initialize] This is biodb version 1.10.0.
biodb.DEBUG[2024-04-13 16:05:52.272][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-04-13 16:05:52.273][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:52.274][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:52.275][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:52.276][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:52.281][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:52.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:52.283][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:52.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:52.284][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:52.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:52.286][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[2024-04-13 16:05:52.287][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:52.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:52.289][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:52.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:52.290][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:52.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:52.292][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:52.293][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:52.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:52.295][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:52.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:52.297][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:52.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:52.298][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:52.299][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:52.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:52.301][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:52.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:52.303][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:52.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:52.304][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:52.305][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:52.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:52.307][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:52.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:52.309][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:52.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:52.310][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:52.311][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:52.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:52.313][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:52.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:52.315][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:52.316][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:52.316][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[2024-04-13 16:05:52.317][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:52.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:52.319][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:52.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:52.321][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:52.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:52.322][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:52.323][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:52.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:52.325][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:52.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:52.327][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:52.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:52.328][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:52.329][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:52.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:52.331][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:52.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:52.333][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:52.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:52.334][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:52.335][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:52.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:52.337][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:52.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:52.338][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:52.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:52.340][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[2024-04-13 16:05:52.341][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:52.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:52.342][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:52.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:52.344][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:52.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:52.345][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:52.346][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:52.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:52.348][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:52.349][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:52.349][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:52.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:52.351][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:52.352][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:52.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:52.353][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:52.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:52.355][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:52.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:52.357][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:52.357][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:52.358][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:52.359][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:52.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:52.361][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:52.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:52.362][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:52.363][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:52.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:52.365][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:52.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:52.366][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:52.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:52.368][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:52.369][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:52.369][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:52.370][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:52.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:52.372][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:52.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:52.373][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:52.374][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:52.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:52.376][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:52.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:52.377][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:52.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:52.379][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:52.380][biodb$getConfig()$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-04-13 16:05:52.381][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-13 16:05:52.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:52.382][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:52.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:52.384][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:52.385][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:52.385][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-13 16:05:52.387][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.18-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/definitions.yml".
biodb.DEBUG[2024-04-13 16:05:52.396][self$getDbsInfo()$define] Define connector hmdb.metabolites.
biodb.DEBUG[2024-04-13 16:05:52.397][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-04-13 16:05:52.398][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-04-13 16:05:52.399][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:52.400][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-13 16:05:52.401][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2024-04-13 16:05:52.402][self$setPropertyValue] Setting property "dwnld.ext" to "zip".
biodb.DEBUG[2024-04-13 16:05:52.403][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:52.404][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-13 16:05:52.405][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-04-13 16:05:52.406][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-13 16:05:52.407][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:52.407][self$setPropertyValue] Setting property "name" to "HMDB Metabolites".
biodb.DEBUG[2024-04-13 16:05:52.408][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-13 16:05:52.409][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/accession".
biodb.DEBUG[2024-04-13 16:05:52.409][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/secondary_accessions/accession".
biodb.DEBUG[2024-04-13 16:05:52.409][self$setPropertyValue] Setting property "parsing.expr" to "//average_molecular_weight".
biodb.DEBUG[2024-04-13 16:05:52.409][self$setPropertyValue] Setting property "parsing.expr" to "//cas_registry_number".
biodb.DEBUG[2024-04-13 16:05:52.409][self$setPropertyValue] Setting property "parsing.expr" to "//chebi_id".
biodb.DEBUG[2024-04-13 16:05:52.409][self$setPropertyValue] Setting property "parsing.expr" to "//chemspider_id".
biodb.DEBUG[2024-04-13 16:05:52.409][self$setPropertyValue] Setting property "parsing.expr" to "//kegg_id".
biodb.DEBUG[2024-04-13 16:05:52.409][self$setPropertyValue] Setting property "parsing.expr" to "//pubchem_compound_id".
biodb.DEBUG[2024-04-13 16:05:52.409][self$setPropertyValue] Setting property "parsing.expr" to "//iupac_name".
biodb.DEBUG[2024-04-13 16:05:52.409][self$setPropertyValue] Setting property "parsing.expr" to "//traditional_iupac".
biodb.DEBUG[2024-04-13 16:05:52.409][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/chemical_formula".
biodb.DEBUG[2024-04-13 16:05:52.409][self$setPropertyValue] Setting property "parsing.expr" to "//inchi".
biodb.DEBUG[2024-04-13 16:05:52.409][self$setPropertyValue] Setting property "parsing.expr" to "//inchikey".
biodb.DEBUG[2024-04-13 16:05:52.409][self$setPropertyValue] Setting property "parsing.expr" to "//monisotopic_molecular_weight".
biodb.DEBUG[2024-04-13 16:05:52.409][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/name".
biodb.DEBUG[2024-04-13 16:05:52.409][self$setPropertyValue] Setting property "parsing.expr" to "/metabolite/description".
biodb.DEBUG[2024-04-13 16:05:52.409][self$setPropertyValue] Setting property "parsing.expr" to "//smiles".
biodb.DEBUG[2024-04-13 16:05:52.409][self$setPropertyValue] Setting property "parsing.expr" to "//super_class".
biodb.DEBUG[2024-04-13 16:05:52.410][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-04-13 16:05:52.411][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-04-13 16:05:52.411][self$setPropertyValue] Setting property "searchable.fields" to "description".
biodb.DEBUG[2024-04-13 16:05:52.411][self$setPropertyValue] Setting property "searchable.fields" to "secondary.accessions".
biodb.DEBUG[2024-04-13 16:05:52.412][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-04-13 16:05:52.413][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-13 16:05:52.414][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-13 16:05:52.419][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-13 16:05:52.420][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-13 16:05:52.421][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-13 16:05:52.422][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-13 16:05:52.422][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/".
biodb.DEBUG[2024-04-13 16:05:52.422][self$setPropertyValue] Setting property "urls" to "http://www.hmdb.ca/system/downloads/current/hmdb_metabolites.zip".
biodb.DEBUG[2024-04-13 16:05:52.423][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-13 16:05:52.424][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-13 16:05:52.425][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-04-13 16:05:52.426][self$setPropertyValue]
biodb.DEBUG[2024-04-13 16:05:52.431][self$getEntryFields()$define] Define field secondary_accessions.
biodb.DEBUG[2024-04-13 16:05:52.432][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-04-13 16:05:52.434][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-04-13 16:05:52.435][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-04-13 16:05:52.437][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-04-13 16:05:52.460][initialize] Initialize connector hmdb.metabolites.
biodb.DEBUG[2024-04-13 16:05:52.461][initialize] Register connector hmdb.metabolites with the request scheduler
biodb.DEBUG[2024-04-13 16:05:52.465][private$bdb$getRequestScheduler()$re ...] Register connector hmdb.metabolites.
biodb.DEBUG[2024-04-13 16:05:52.469][private$addConnectorRules] Create new rule for URL "www.hmdb.ca" of connector "hmdb.metabolites".
biodb.DEBUG[2024-04-13 16:05:52.473][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-04-13 16:05:52.474][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-04-13 16:05:52.475][rule$addConnector] Connector "hmdb.metabolites" is already listed in rule "www.hmdb.ca".
biodb.DEBUG[2024-04-13 16:05:52.476][biodb$getFactory()$createConn] Creating new connector hmdb.metabolites for database class hmdb.metabolites .
biodb.INFO [2024-04-13 16:05:52.485][biodb::testThat]
biodb.INFO [2024-04-13 16:05:52.486][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value ").
biodb.INFO [2024-04-13 16:05:52.487][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-13 16:05:52.488][biodb::testThat]
biodb.TRACE[2024-04-13 16:05:52.492][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.18-bioc-longtests/meat/biodbHmdb.Rcheck/biodbHmdb/testref/entry-hmdb.metabolites-HMDB0000001-content.xml".
biodb.DEBUG[2024-04-13 16:05:52.494][biodb$getFactory()$createEntryFromCo ...] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2024-04-13 16:05:52.497][biodb$getFactory()$createEntryFromCo ...] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2024-04-13 16:05:52.506][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-13 16:05:52.506][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:52.507][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:52.519][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:52.519][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:52.520][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:52.521][FUN] Functions in observer BiodbConfig: [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[2024-04-13 16:05:52.533][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:52.534][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:52.535][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:52.536][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:52.537][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:52.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:52.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:52.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:52.552][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-04-13 16:05:52.553][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-04-13 16:05:52.554][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:52.555][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:52.578][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-04-13 16:05:52.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-04-13 16:05:52.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:52.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:52.582][ef$get] Asked field names are: average.mass.
biodb.TRACE[2024-04-13 16:05:52.583][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-04-13 16:05:52.584][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:52.585][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:52.586][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-04-13 16:05:52.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-04-13 16:05:52.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:52.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:52.590][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-04-13 16:05:52.591][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-04-13 16:05:52.592][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:52.593][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:52.594][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-04-13 16:05:52.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-04-13 16:05:52.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:52.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:52.598][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-13 16:05:52.598][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-13 16:05:52.599][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:52.600][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:52.601][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-13 16:05:52.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-13 16:05:52.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:52.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:52.605][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-04-13 16:05:52.606][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-04-13 16:05:52.607][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:52.608][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:52.609][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-04-13 16:05:52.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-04-13 16:05:52.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:52.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:52.613][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-13 16:05:52.614][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-13 16:05:52.615][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:52.615][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:52.617][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-13 16:05:52.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-13 16:05:52.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:52.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:52.629][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-13 16:05:52.630][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-13 16:05:52.631][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:52.632][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:52.633][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-13 16:05:52.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-13 16:05:52.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:52.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:52.636][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-04-13 16:05:52.637][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-04-13 16:05:52.638][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:52.639][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:52.640][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-04-13 16:05:52.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-04-13 16:05:52.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:52.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:52.644][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-04-13 16:05:52.645][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-04-13 16:05:52.645][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:52.646][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:52.647][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-04-13 16:05:52.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-04-13 16:05:52.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:52.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:52.651][ef$get] Asked field names are: formula.
biodb.TRACE[2024-04-13 16:05:52.652][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-13 16:05:52.653][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:52.654][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:52.655][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-13 16:05:52.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-13 16:05:52.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:52.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:52.658][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-04-13 16:05:52.659][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-13 16:05:52.660][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:52.661][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:52.662][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-04-13 16:05:52.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-13 16:05:52.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:52.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:52.666][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-13 16:05:52.667][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-13 16:05:52.668][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:52.669][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:52.670][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-13 16:05:52.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-13 16:05:52.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:52.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:52.673][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-13 16:05:52.674][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-13 16:05:52.675][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:52.676][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:52.677][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-13 16:05:52.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-13 16:05:52.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:52.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:52.681][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:52.682][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:52.683][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:52.684][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:52.685][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:52.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:52.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:52.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:52.688][ef$get] Asked field names are: description.
biodb.TRACE[2024-04-13 16:05:52.689][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-04-13 16:05:52.690][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:52.691][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:52.692][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-04-13 16:05:52.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-04-13 16:05:52.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:52.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:52.696][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-04-13 16:05:52.697][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-13 16:05:52.698][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:52.698][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:52.700][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-04-13 16:05:52.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-13 16:05:52.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:52.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:52.703][ef$get] Asked field names are: super.class.
biodb.TRACE[2024-04-13 16:05:52.704][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-04-13 16:05:52.705][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:52.706][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:52.707][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2024-04-13 16:05:52.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-04-13 16:05:52.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:52.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:52.711][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:52.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:52.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:52.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:52.714][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:52.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:52.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:52.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:52.718][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:52.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:52.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:52.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:52.751][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-04-13 16:05:52.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-04-13 16:05:52.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:52.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:52.755][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-04-13 16:05:52.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-04-13 16:05:52.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:52.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:52.758][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-04-13 16:05:52.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-04-13 16:05:52.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:52.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:52.762][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-04-13 16:05:52.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-04-13 16:05:52.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:52.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:52.766][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-04-13 16:05:52.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-04-13 16:05:52.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:52.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:52.769][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-04-13 16:05:52.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-04-13 16:05:52.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:52.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:52.805][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-13 16:05:52.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-13 16:05:52.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:52.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:52.809][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-13 16:05:52.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-13 16:05:52.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:52.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:52.812][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-13 16:05:52.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-13 16:05:52.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:52.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:52.816][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-04-13 16:05:52.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-04-13 16:05:52.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:52.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:52.820][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-04-13 16:05:52.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-04-13 16:05:52.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:52.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:52.823][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-04-13 16:05:52.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-04-13 16:05:52.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:52.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:52.827][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-04-13 16:05:52.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-04-13 16:05:52.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:52.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:52.830][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-04-13 16:05:52.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-04-13 16:05:52.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:52.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:52.834][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-04-13 16:05:52.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-04-13 16:05:52.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:52.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:52.838][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-04-13 16:05:52.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-04-13 16:05:52.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:52.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:52.841][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-04-13 16:05:52.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-04-13 16:05:52.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:52.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:52.845][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-04-13 16:05:52.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-04-13 16:05:52.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:52.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:52.849][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-04-13 16:05:52.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-04-13 16:05:52.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:52.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:52.852][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-04-13 16:05:52.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-04-13 16:05:52.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:52.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:52.856][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-04-13 16:05:52.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-04-13 16:05:52.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:52.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:52.860][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-04-13 16:05:52.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-04-13 16:05:52.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:52.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:52.863][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-04-13 16:05:52.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-04-13 16:05:52.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:52.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:52.867][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-04-13 16:05:52.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-04-13 16:05:52.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:52.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:52.870][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-13 16:05:52.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-13 16:05:52.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:52.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:52.874][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-13 16:05:52.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-13 16:05:52.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:52.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:52.878][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-13 16:05:52.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-13 16:05:52.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:52.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:52.881][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-04-13 16:05:52.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-13 16:05:52.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:52.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:52.885][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-04-13 16:05:52.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-13 16:05:52.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:52.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:52.888][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-04-13 16:05:52.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-13 16:05:52.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:52.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:52.892][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-13 16:05:52.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-13 16:05:52.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:52.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:52.896][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-13 16:05:52.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-13 16:05:52.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:52.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:52.899][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-13 16:05:52.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-13 16:05:52.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:52.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:52.903][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-13 16:05:52.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-13 16:05:52.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:52.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:52.907][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-13 16:05:52.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-13 16:05:52.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:52.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:52.910][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-13 16:05:52.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-13 16:05:52.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:52.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:52.914][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-13 16:05:52.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-13 16:05:52.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:52.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:52.917][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-13 16:05:52.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-13 16:05:52.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:52.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:52.921][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-13 16:05:52.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-13 16:05:52.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:52.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:52.925][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:52.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:52.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:52.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:52.928][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:52.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:52.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:52.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:52.932][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:52.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:52.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:52.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:52.936][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-13 16:05:52.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-13 16:05:52.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:52.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:52.939][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-13 16:05:52.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-13 16:05:52.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:52.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:52.943][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-13 16:05:52.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-13 16:05:52.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:52.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:52.946][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-04-13 16:05:52.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-04-13 16:05:52.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:52.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:52.950][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-04-13 16:05:52.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-04-13 16:05:52.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:52.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:52.954][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-04-13 16:05:52.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-04-13 16:05:52.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:52.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:52.961][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-04-13 16:05:52.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-13 16:05:52.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:52.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:52.964][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-04-13 16:05:52.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-13 16:05:52.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:52.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:52.968][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-04-13 16:05:52.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-13 16:05:52.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:52.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:52.971][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2024-04-13 16:05:52.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-13 16:05:52.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:52.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:52.975][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-13 16:05:52.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-13 16:05:52.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:52.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:52.978][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-13 16:05:52.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-13 16:05:52.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:52.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:52.982][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-13 16:05:52.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-13 16:05:52.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:52.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:52.986][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2024-04-13 16:05:52.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-13 16:05:52.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:52.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.005][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:53.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:53.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.009][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:53.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:53.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.012][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:53.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:53.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.016][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:53.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:53.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.020][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:53.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:53.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.023][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-04-13 16:05:53.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-04-13 16:05:53.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.027][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-04-13 16:05:53.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-04-13 16:05:53.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.030][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:53.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:53.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.034][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-04-13 16:05:53.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-04-13 16:05:53.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.038][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:53.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:53.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.041][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:53.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:53.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.045][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:53.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:53.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.049][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:53.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:53.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.052][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:53.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:53.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.056][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:53.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:53.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-13 16:05:53.059][biodb$getFactory()$createEntryFromCo ...] Accession numbers: HMDB0000001.
biodb.TRACE[2024-04-13 16:05:53.062][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-04-13 16:05:53.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-04-13 16:05:53.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.065][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-04-13 16:05:53.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-04-13 16:05:53.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.069][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-04-13 16:05:53.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-04-13 16:05:53.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.072][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-04-13 16:05:53.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-04-13 16:05:53.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.090][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:53.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:53.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.104][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-04-13 16:05:53.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-04-13 16:05:53.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.115][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:53.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:53.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.119][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:53.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:53.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.122][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:53.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:53.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.128][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:53.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:53.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.131][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:53.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:53.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.135][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:53.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:53.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.139][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-04-13 16:05:53.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-04-13 16:05:53.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.142][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-04-13 16:05:53.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-04-13 16:05:53.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.146][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-04-13 16:05:53.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-04-13 16:05:53.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.156][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:53.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:53.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.160][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:53.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:53.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.163][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:53.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:53.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.167][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:53.168][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:53.169][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.169][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.170][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:53.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:53.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.181][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-04-13 16:05:53.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-04-13 16:05:53.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.185][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-04-13 16:05:53.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-04-13 16:05:53.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.188][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-04-13 16:05:53.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-04-13 16:05:53.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.192][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-04-13 16:05:53.193][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-04-13 16:05:53.194][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.195][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.195][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-04-13 16:05:53.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-04-13 16:05:53.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.206][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-04-13 16:05:53.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-04-13 16:05:53.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.209][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-04-13 16:05:53.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-04-13 16:05:53.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.213][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-04-13 16:05:53.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-04-13 16:05:53.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.217][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-04-13 16:05:53.218][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-04-13 16:05:53.219][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.219][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.220][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-04-13 16:05:53.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-04-13 16:05:53.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.231][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-13 16:05:53.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-13 16:05:53.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.234][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-13 16:05:53.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-13 16:05:53.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.238][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-13 16:05:53.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-13 16:05:53.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.242][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-13 16:05:53.243][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-13 16:05:53.243][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.244][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.245][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-13 16:05:53.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-13 16:05:53.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.255][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-13 16:05:53.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-13 16:05:53.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.259][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-13 16:05:53.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-13 16:05:53.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.267][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-13 16:05:53.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-13 16:05:53.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.270][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-13 16:05:53.271][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-13 16:05:53.272][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.273][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.274][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-13 16:05:53.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-13 16:05:53.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.284][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-13 16:05:53.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-13 16:05:53.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.287][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-13 16:05:53.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-13 16:05:53.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.291][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-13 16:05:53.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-13 16:05:53.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.294][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-13 16:05:53.295][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-13 16:05:53.296][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.297][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.298][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-13 16:05:53.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-13 16:05:53.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.308][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:53.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:53.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.312][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:53.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:53.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.315][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:53.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:53.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.319][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:53.320][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:53.321][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.321][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.322][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:53.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:53.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.332][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-04-13 16:05:53.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-04-13 16:05:53.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.336][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-04-13 16:05:53.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-04-13 16:05:53.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.339][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-04-13 16:05:53.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-04-13 16:05:53.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.343][ef$get] Asked field names are: description.
biodb.TRACE[2024-04-13 16:05:53.344][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-04-13 16:05:53.345][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.346][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.347][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-04-13 16:05:53.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-04-13 16:05:53.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.357][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-13 16:05:53.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-13 16:05:53.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.360][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-13 16:05:53.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-13 16:05:53.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.364][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-13 16:05:53.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-13 16:05:53.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.368][ef$get] Asked field names are: formula.
biodb.TRACE[2024-04-13 16:05:53.369][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-13 16:05:53.369][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.370][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.371][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-13 16:05:53.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-13 16:05:53.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.381][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-04-13 16:05:53.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-04-13 16:05:53.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.385][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-04-13 16:05:53.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-04-13 16:05:53.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.389][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-04-13 16:05:53.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-04-13 16:05:53.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.392][ef$get] Asked field names are: average.mass.
biodb.TRACE[2024-04-13 16:05:53.393][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-04-13 16:05:53.394][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.395][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.396][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-04-13 16:05:53.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-04-13 16:05:53.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.406][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-13 16:05:53.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-13 16:05:53.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.409][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-13 16:05:53.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-13 16:05:53.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.417][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-13 16:05:53.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-13 16:05:53.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.420][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-13 16:05:53.421][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-13 16:05:53.422][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.423][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.424][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-13 16:05:53.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-13 16:05:53.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.434][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-04-13 16:05:53.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-04-13 16:05:53.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.437][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-04-13 16:05:53.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-04-13 16:05:53.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.441][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-04-13 16:05:53.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-04-13 16:05:53.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.445][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-04-13 16:05:53.446][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-04-13 16:05:53.446][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.447][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.448][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-04-13 16:05:53.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-04-13 16:05:53.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.458][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-04-13 16:05:53.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-04-13 16:05:53.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.462][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-04-13 16:05:53.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-04-13 16:05:53.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.465][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-04-13 16:05:53.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-04-13 16:05:53.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.469][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-04-13 16:05:53.470][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-04-13 16:05:53.471][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.472][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.473][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-04-13 16:05:53.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-04-13 16:05:53.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.483][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-04-13 16:05:53.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-04-13 16:05:53.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.486][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-04-13 16:05:53.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-04-13 16:05:53.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.490][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-04-13 16:05:53.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-04-13 16:05:53.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.493][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-04-13 16:05:53.494][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-04-13 16:05:53.495][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.496][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.497][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-04-13 16:05:53.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-04-13 16:05:53.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.507][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-04-13 16:05:53.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-13 16:05:53.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.510][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-04-13 16:05:53.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-13 16:05:53.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.514][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-04-13 16:05:53.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-13 16:05:53.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.518][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-04-13 16:05:53.518][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-13 16:05:53.519][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.520][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.521][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-04-13 16:05:53.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-13 16:05:53.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.531][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-04-13 16:05:53.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-13 16:05:53.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.535][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-04-13 16:05:53.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-13 16:05:53.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.538][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-04-13 16:05:53.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-13 16:05:53.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.542][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-04-13 16:05:53.543][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-13 16:05:53.544][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.544][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.545][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-04-13 16:05:53.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-13 16:05:53.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.555][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-13 16:05:53.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-13 16:05:53.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.559][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-13 16:05:53.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-13 16:05:53.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.566][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-13 16:05:53.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-13 16:05:53.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.570][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-13 16:05:53.571][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-13 16:05:53.572][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.572][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.573][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-13 16:05:53.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-13 16:05:53.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.583][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-04-13 16:05:53.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-04-13 16:05:53.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.587][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-04-13 16:05:53.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-04-13 16:05:53.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.590][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-04-13 16:05:53.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-04-13 16:05:53.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.594][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-04-13 16:05:53.595][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-04-13 16:05:53.596][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.596][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.597][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-04-13 16:05:53.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-04-13 16:05:53.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.607][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:53.608][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:53.609][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.610][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.614][ef$get] Asked field names are: average.mass.
biodb.TRACE[2024-04-13 16:05:53.615][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-04-13 16:05:53.616][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.616][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.620][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-04-13 16:05:53.621][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-04-13 16:05:53.622][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.623][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.626][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-13 16:05:53.627][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-13 16:05:53.628][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.629][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.633][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-04-13 16:05:53.634][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-04-13 16:05:53.635][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.635][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.639][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-04-13 16:05:53.640][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-04-13 16:05:53.641][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.642][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.645][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-04-13 16:05:53.646][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-04-13 16:05:53.647][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.648][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.652][ef$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-04-13 16:05:53.653][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-04-13 16:05:53.654][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.654][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.658][ef$get] Asked field names are: description.
biodb.TRACE[2024-04-13 16:05:53.659][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-04-13 16:05:53.660][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.661][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.664][ef$get] Asked field names are: formula.
biodb.TRACE[2024-04-13 16:05:53.665][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-13 16:05:53.666][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.667][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.671][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-04-13 16:05:53.672][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-13 16:05:53.673][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.674][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.677][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-13 16:05:53.678][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-13 16:05:53.679][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.680][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.684][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-13 16:05:53.684][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-13 16:05:53.685][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.686][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.690][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-13 16:05:53.691][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-13 16:05:53.692][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.693][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.696][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:53.697][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:53.698][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.699][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.703][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-13 16:05:53.703][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-13 16:05:53.704][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.705][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.713][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-04-13 16:05:53.714][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-04-13 16:05:53.715][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.715][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.719][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-04-13 16:05:53.720][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-13 16:05:53.721][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.722][ef$get] fields variable is a list.
biodb.INFO [2024-04-13 16:05:53.728][biodb::testThat]
biodb.INFO [2024-04-13 16:05:53.729][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-04-13 16:05:53.729][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-13 16:05:53.730][biodb::testThat]
biodb.DEBUG[2024-04-13 16:05:53.743][private$loadEntries] Creating entries from ids [1]: "HMDB0000001".
biodb.DEBUG[2024-04-13 16:05:53.750][conn$getEntryContent] Get HMDB Metabolites entry content(s) for 1 id(s)...
biodb.DEBUG[2024-04-13 16:05:53.754][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-04-13 16:05:53.755][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.TRACE[2024-04-13 16:05:53.757][cch$loadFileContent] Trying to load 1 files from cache: [1]: "HMDB0000001".
biodb.TRACE[2024-04-13 16:05:53.758][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-13 16:05:53.761][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34/HMDB0000001.xml".
biodb.DEBUG[2024-04-13 16:05:53.762][conn$getEntryContent] 1 HMDB Metabolites entry content(s) loaded from cache.
biodb.DEBUG[2024-04-13 16:05:53.783][self$createEntryFromContent] Creating HMDB Metabolites entries from 1 content(s).
biodb.DEBUG[2024-04-13 16:05:53.784][self$createEntryFromContent] Parsing 1 HMDB Metabolites entries.
biodb.DEBUG[2024-04-13 16:05:53.786][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-13 16:05:53.786][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:53.787][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:53.791][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:53.792][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:53.793][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:53.794][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-13 16:05:53.797][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:53.798][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:53.799][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.800][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.801][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:53.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:53.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.805][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-04-13 16:05:53.806][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-04-13 16:05:53.807][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.807][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.809][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-04-13 16:05:53.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-04-13 16:05:53.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.812][ef$get] Asked field names are: average.mass.
biodb.TRACE[2024-04-13 16:05:53.813][ef$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-04-13 16:05:53.814][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.815][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.816][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-04-13 16:05:53.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-04-13 16:05:53.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.820][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-04-13 16:05:53.821][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-04-13 16:05:53.822][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.823][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.824][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-04-13 16:05:53.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-04-13 16:05:53.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.827][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-13 16:05:53.828][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-13 16:05:53.829][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.830][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.831][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-13 16:05:53.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-13 16:05:53.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.835][ef$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-04-13 16:05:53.836][ef$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-04-13 16:05:53.837][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.838][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.839][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-04-13 16:05:53.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-04-13 16:05:53.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.842][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-13 16:05:53.843][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-13 16:05:53.844][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.845][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.846][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-13 16:05:53.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-13 16:05:53.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.850][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-13 16:05:53.851][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-13 16:05:53.852][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.853][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.854][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-13 16:05:53.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-13 16:05:53.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.857][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-04-13 16:05:53.858][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-04-13 16:05:53.864][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.865][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.866][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-04-13 16:05:53.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-04-13 16:05:53.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.870][ef$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-04-13 16:05:53.871][ef$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-04-13 16:05:53.872][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.872][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.874][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-04-13 16:05:53.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-04-13 16:05:53.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.877][ef$get] Asked field names are: formula.
biodb.TRACE[2024-04-13 16:05:53.878][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-13 16:05:53.879][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.880][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.881][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-13 16:05:53.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-13 16:05:53.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.885][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-04-13 16:05:53.885][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-13 16:05:53.886][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.887][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.888][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-04-13 16:05:53.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-13 16:05:53.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.892][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-13 16:05:53.893][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-13 16:05:53.894][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.895][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.896][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-13 16:05:53.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-13 16:05:53.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.900][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-13 16:05:53.901][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-13 16:05:53.901][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.902][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.903][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-13 16:05:53.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-13 16:05:53.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.907][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:53.908][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:53.909][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.910][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.911][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:53.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:53.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.914][ef$get] Asked field names are: description.
biodb.TRACE[2024-04-13 16:05:53.915][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-04-13 16:05:53.916][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.917][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.918][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-04-13 16:05:53.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-04-13 16:05:53.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.922][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-04-13 16:05:53.923][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-13 16:05:53.924][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.924][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.926][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-04-13 16:05:53.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-13 16:05:53.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.929][ef$get] Asked field names are: super.class.
biodb.TRACE[2024-04-13 16:05:53.930][ef$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-04-13 16:05:53.931][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.932][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.933][self$getBiodb()$getEntryFields()$get] Asked field names are: super.class.
biodb.TRACE[2024-04-13 16:05:53.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-04-13 16:05:53.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.937][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:53.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:53.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.940][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:53.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:53.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.944][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:53.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:53.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.948][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-04-13 16:05:53.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-04-13 16:05:53.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.951][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-04-13 16:05:53.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-04-13 16:05:53.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.955][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-04-13 16:05:53.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-04-13 16:05:53.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.959][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-04-13 16:05:53.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-04-13 16:05:53.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.962][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-04-13 16:05:53.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-04-13 16:05:53.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.966][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-04-13 16:05:53.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-04-13 16:05:53.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.969][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-13 16:05:53.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-13 16:05:53.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.973][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-13 16:05:53.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-13 16:05:53.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.976][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-13 16:05:53.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-13 16:05:53.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.980][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-04-13 16:05:53.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-04-13 16:05:53.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.984][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-04-13 16:05:53.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-04-13 16:05:53.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.987][self$getBiodb()$getEntryFields()$get] Asked field names are: chemspider.id.
biodb.TRACE[2024-04-13 16:05:53.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chemspider.id.
biodb.TRACE[2024-04-13 16:05:53.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.991][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-04-13 16:05:53.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-04-13 16:05:53.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.994][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-04-13 16:05:53.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-04-13 16:05:53.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:53.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:53.998][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-04-13 16:05:53.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-04-13 16:05:54.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:54.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:54.002][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-04-13 16:05:54.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-04-13 16:05:54.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:54.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:54.005][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-04-13 16:05:54.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-04-13 16:05:54.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:54.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:54.013][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.trad.
biodb.TRACE[2024-04-13 16:05:54.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.trad.
biodb.TRACE[2024-04-13 16:05:54.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:54.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:54.016][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-04-13 16:05:54.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-04-13 16:05:54.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:54.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:54.020][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-04-13 16:05:54.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-04-13 16:05:54.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:54.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:54.023][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.super.class.
biodb.TRACE[2024-04-13 16:05:54.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.super.class.
biodb.TRACE[2024-04-13 16:05:54.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:54.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:54.027][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-04-13 16:05:54.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-04-13 16:05:54.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:54.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:54.030][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-04-13 16:05:54.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-04-13 16:05:54.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:54.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:54.034][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-04-13 16:05:54.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-04-13 16:05:54.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:54.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:54.037][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-13 16:05:54.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-13 16:05:54.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:54.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:54.041][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-13 16:05:54.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-13 16:05:54.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:54.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:54.045][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-13 16:05:54.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-13 16:05:54.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:54.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:54.048][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-04-13 16:05:54.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-13 16:05:54.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:54.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:54.052][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-04-13 16:05:54.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-13 16:05:54.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:54.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:54.056][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-04-13 16:05:54.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-13 16:05:54.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:54.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:54.059][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-13 16:05:54.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-13 16:05:54.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:54.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:54.063][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-13 16:05:54.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-13 16:05:54.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:54.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:54.066][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-13 16:05:54.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-13 16:05:54.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:54.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:54.070][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-13 16:05:54.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-13 16:05:54.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:54.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:54.074][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-13 16:05:54.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-13 16:05:54.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:54.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:54.077][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-13 16:05:54.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-13 16:05:54.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:54.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:54.081][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-13 16:05:54.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-13 16:05:54.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:54.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:54.084][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-13 16:05:54.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-13 16:05:54.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:54.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:54.088][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-13 16:05:54.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-13 16:05:54.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:54.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:54.092][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:54.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:54.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:54.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:54.095][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:54.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:54.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:54.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:54.099][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:54.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:54.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:54.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:54.102][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-13 16:05:54.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-13 16:05:54.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:54.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:54.106][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-13 16:05:54.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-13 16:05:54.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:54.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:54.110][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-13 16:05:54.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-13 16:05:54.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:54.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:54.113][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-04-13 16:05:54.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-04-13 16:05:54.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:54.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:54.117][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-04-13 16:05:54.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-04-13 16:05:54.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:54.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:54.120][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-04-13 16:05:54.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-04-13 16:05:54.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:54.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:54.124][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-04-13 16:05:54.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-13 16:05:54.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:54.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:54.128][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-04-13 16:05:54.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-13 16:05:54.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:54.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:54.131][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-04-13 16:05:54.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-13 16:05:54.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:54.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:54.135][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2024-04-13 16:05:54.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-13 16:05:54.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:54.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:54.138][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-13 16:05:54.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-13 16:05:54.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:54.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:54.142][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-13 16:05:54.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-13 16:05:54.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:54.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:54.146][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-13 16:05:54.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-13 16:05:54.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:54.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:54.149][self$getBiodb()$getEntryFields()$get] Asked field names are: INCHIKEY.
biodb.TRACE[2024-04-13 16:05:54.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-13 16:05:54.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:54.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:54.154][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:54.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:54.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:54.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:54.161][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:54.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:54.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:54.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:54.164][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:54.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:54.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:54.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:54.168][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:54.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:54.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:54.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:54.171][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:54.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:54.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:54.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:54.175][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-04-13 16:05:54.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-04-13 16:05:54.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:54.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:54.179][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-04-13 16:05:54.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-04-13 16:05:54.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:54.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:54.182][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:54.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:54.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:54.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:54.186][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-04-13 16:05:54.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-04-13 16:05:54.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:54.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:54.189][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:54.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:54.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:54.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:54.193][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:54.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:54.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:54.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:54.197][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:54.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:54.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:54.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:54.200][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:54.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:54.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:54.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:54.204][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:54.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:54.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:54.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:54.208][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-13 16:05:54.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-13 16:05:54.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:54.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-13 16:05:54.211][self$createEntryFromContent] Accession numbers: HMDB0000001.
biodb.TRACE[2024-04-13 16:05:54.212][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-04-13 16:05:54.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-04-13 16:05:54.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:54.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:54.216][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-04-13 16:05:54.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-04-13 16:05:54.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:54.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:54.219][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-04-13 16:05:54.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-04-13 16:05:54.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:54.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-04-13 16:05:54.229][biodb::testThat]
biodb.INFO [2024-04-13 16:05:54.230][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field ").
biodb.INFO [2024-04-13 16:05:54.231][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-13 16:05:54.232][biodb::testThat]
biodb.TRACE[2024-04-13 16:05:54.234][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:54.235][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:54.236][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:54.237][ef$get] fields variable is a list.
biodb.DEBUG[2024-04-13 16:05:54.238][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "name".
biodb.TRACE[2024-04-13 16:05:54.259][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:54.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:54.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:54.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:54.263][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:54.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:54.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:54.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:54.267][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:54.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:54.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:54.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-13 16:05:54.273][function(conn, opt)] With value "1-Methylhistidine".
biodb.DEBUG[2024-04-13 16:05:54.274][private$doSearchForEntries] fields NAMES = name
biodb.DEBUG[2024-04-13 16:05:54.275][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2024-04-13 16:05:54.276][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2024-04-13 16:05:54.277][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-04-13 16:05:54.278][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-04-13 16:05:54.280][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2024-04-13 16:05:54.281][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-04-13 16:05:54.282][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2024-04-13 16:05:54.283][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2024-04-13 16:05:54.284][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2024-04-13 16:05:54.285][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2024-04-13 16:05:54.286][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2024-04-13 16:05:54.287][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2024-04-13 16:05:54.288][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2024-04-13 16:05:54.289][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:54.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:54.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:54.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:54.293][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:54.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:54.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:54.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:54.297][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:54.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:54.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:54.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:54.304][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:54.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:54.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:54.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-13 16:05:54.308][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2024-04-13 16:05:54.308][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2024-04-13 16:05:54.309][function(conn, opt)] With found IDs [1]: "HMDB0000001".
biodb.TRACE[2024-04-13 16:05:54.319][ef$get] Asked field names are: description.
biodb.TRACE[2024-04-13 16:05:54.320][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-04-13 16:05:54.320][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:54.321][ef$get] fields variable is a list.
biodb.DEBUG[2024-04-13 16:05:54.322][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "description".
biodb.TRACE[2024-04-13 16:05:54.332][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-04-13 16:05:54.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-04-13 16:05:54.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:54.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:54.335][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-04-13 16:05:54.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-04-13 16:05:54.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:54.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:54.339][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-04-13 16:05:54.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-04-13 16:05:54.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:54.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-13 16:05:54.345][function(conn, opt)] With value "1-Methylhistidine, also known as 1-MHis, belongs to the class of organic compounds known as histidine and derivatives. Histidine and derivatives are compounds containing cysteine or a derivative thereof resulting from a reaction of cysteine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. 1-Methylhistidine is derived mainly from the anserine of dietary flesh sources, especially poultry. The enzyme, carnosinase, splits anserine into beta-alanine and 1-MHis. High levels of 1-MHis tend to inhibit the enzyme carnosinase and increase anserine levels. Conversely, genetic variants with deficient carnosinase activity in plasma show increased 1-MHis excretions when they consume a high meat diet. Reduced serum carnosinase activity is also found in patients with Parkinson's disease and multiple sclerosis and patients following a cerebrovascular accident. Vitamin E deficiency can lead to 1-methylhistidinuria from increased oxidative effects in skeletal muscle. 1-Methylhistidine is a biomarker for the consumption of meat, especially red meat.".
biodb.DEBUG[2024-04-13 16:05:54.392][private$doSearchForEntries] fields NAMES = description
biodb.DEBUG[2024-04-13 16:05:54.393][private$doSearchForEntries] fields VALUES = 1-Methylhistidine, also known as 1-MHis, belongs to the class of organic compounds known as histidine and derivatives. Histidine and derivatives are compounds containing cysteine or a derivative thereof resulting from a reaction of cysteine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. 1-Methylhistidine is derived mainly from the anserine of dietary flesh sources, especially poultry. The enzyme, carnosinase, splits anserine into beta-alanine and 1-MHis. High levels of 1-MHis tend to inhibit the enzyme carnosinase and increase anserine levels. Conversely, genetic variants with deficient carnosinase activity in plasma show increased 1-MHis excretions when they consume a high meat diet. Reduced serum carnosinase activity is also found in patients with Parkinson's disease and multiple sclerosis and patients following a cerebrovascular accident. Vitamin E deficiency can lead to 1-methylhistidinuria from increased oxidative effects in skeletal muscle. 1-Methylhistidine is a biomarker for the consumption of meat, especially red meat.
biodb.DEBUG[2024-04-13 16:05:54.393][private$doSearchForEntries] fields VALUES = 1-Methylhistidine, also known as 1-MHis, belongs to the class of organic compounds known as histidine and derivatives. Histidine and derivatives are compounds containing cysteine or a derivative thereof resulting from a reaction of cysteine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. 1-Methylhistidine is derived mainly from the anserine of dietary flesh sources, especially poultry. The enzyme, carnosinase, splits anserine into beta-alanine and 1-MHis. High levels of 1-MHis tend to inhibit the enzyme carnosinase and increase anserine levels. Conversely, genetic variants with deficient carnosinase activity in plasma show increased 1-MHis excretions when they consume a high meat diet. Reduced serum carnosinase activity is also found in patients with Parkinson's disease and multiple sclerosis and patients following a cerebrovascular accident. Vitamin E deficiency can lead to 1-methylhistidinuria from increased oxidative effects in skeletal muscle. 1-Methylhistidine is a biomarker for the consumption of meat, especially red meat.
biodb.DEBUG[2024-04-13 16:05:54.406][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-04-13 16:05:54.407][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-04-13 16:05:54.408][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2024-04-13 16:05:54.410][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-04-13 16:05:54.411][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2024-04-13 16:05:54.428][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2024-04-13 16:05:54.429][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2024-04-13 16:05:54.430][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2024-04-13 16:05:54.431][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2024-04-13 16:05:54.432][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2024-04-13 16:05:54.432][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2024-04-13 16:05:54.434][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-04-13 16:05:54.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-04-13 16:05:54.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:54.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:54.438][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-04-13 16:05:54.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-04-13 16:05:54.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:54.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:54.441][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-04-13 16:05:54.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-04-13 16:05:54.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:54.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:54.445][self$getBiodb()$getEntryFields()$get] Asked field names are: description.
biodb.TRACE[2024-04-13 16:05:54.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: description.
biodb.TRACE[2024-04-13 16:05:54.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:54.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-13 16:05:54.448][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2024-04-13 16:05:54.449][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2024-04-13 16:05:54.450][function(conn, opt)] With found IDs [1]: "HMDB0000001".
biodb.TRACE[2024-04-13 16:05:54.460][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-04-13 16:05:54.461][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-04-13 16:05:54.462][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:54.463][ef$get] fields variable is a list.
biodb.DEBUG[2024-04-13 16:05:54.464][function(conn, opt)] Testing searchForEntries() with entry "HMDB0000001" and field "secondary.accessions".
biodb.TRACE[2024-04-13 16:05:54.473][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-04-13 16:05:54.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-04-13 16:05:54.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:54.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:54.477][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-04-13 16:05:54.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-04-13 16:05:54.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:54.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:54.480][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-04-13 16:05:54.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-04-13 16:05:54.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:54.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-13 16:05:54.486][function(conn, opt)] With value "HMDB00001".
biodb.DEBUG[2024-04-13 16:05:54.487][private$doSearchForEntries] fields NAMES = secondary.accessions
biodb.DEBUG[2024-04-13 16:05:54.488][private$doSearchForEntries] fields VALUES = HMDB00001
biodb.DEBUG[2024-04-13 16:05:54.489][private$doSearchForEntries] fields VALUES = HMDB00001
biodb.DEBUG[2024-04-13 16:05:54.491][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-04-13 16:05:54.492][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-04-13 16:05:54.493][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2024-04-13 16:05:54.494][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-04-13 16:05:54.495][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2024-04-13 16:05:54.496][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2024-04-13 16:05:54.497][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2024-04-13 16:05:54.498][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2024-04-13 16:05:54.499][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2024-04-13 16:05:54.500][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2024-04-13 16:05:54.501][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2024-04-13 16:05:54.502][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-04-13 16:05:54.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-04-13 16:05:54.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:54.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:54.506][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-04-13 16:05:54.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-04-13 16:05:54.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:54.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:54.510][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-04-13 16:05:54.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-04-13 16:05:54.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:54.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:54.513][self$getBiodb()$getEntryFields()$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-04-13 16:05:54.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-04-13 16:05:54.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:54.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-13 16:05:54.517][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2024-04-13 16:05:54.518][private$doSearchForEntries] COUNT IDS = 1
biodb.DEBUG[2024-04-13 16:05:54.519][function(conn, opt)] With found IDs [1]: "HMDB0000001".
biodb.INFO [2024-04-13 16:05:54.531][biodb::testThat]
biodb.INFO [2024-04-13 16:05:54.532][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. ").
biodb.INFO [2024-04-13 16:05:54.532][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-13 16:05:54.533][biodb::testThat]
biodb.TRACE[2024-04-13 16:05:54.542][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:54.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:54.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:54.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:54.546][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:54.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:54.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:54.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:54.549][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:54.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:54.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:54.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-13 16:05:54.562][private$doSearchForEntries] fields NAMES = name
biodb.DEBUG[2024-04-13 16:05:54.563][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2024-04-13 16:05:54.564][private$doSearchForEntries] fields VALUES = 1-Methylhistidine
biodb.DEBUG[2024-04-13 16:05:54.566][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-04-13 16:05:54.567][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-04-13 16:05:54.568][private$doGetEntryIds] .doGetEntryIds 10
biodb.DEBUG[2024-04-13 16:05:54.570][self$isDownloaded] Database hmdb.metabolites has already been downloaded.
biodb.DEBUG[2024-04-13 16:05:54.570][private$doGetEntryIds] .doGetEntryIds 11
biodb.DEBUG[2024-04-13 16:05:54.576][private$doListFiles] List files in /home/biocbuild/.cache/R/biodb/hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^.*\.xml$.
biodb.DEBUG[2024-04-13 16:05:54.577][cch$listFiles] Extracting accession number from file names associated with hmdb.metabolites-9e094cf1e5980f9ac69d952373fb6d34 using pattern ^(.*)\.xml$
biodb.DEBUG[2024-04-13 16:05:54.578][cch$listFiles] files = HMDB0000001.xml, HMDB0000002.xml
biodb.DEBUG[2024-04-13 16:05:54.578][private$doGetEntryIds] COUNT IDS = 2
biodb.DEBUG[2024-04-13 16:05:54.579][private$doSearchForEntries] All IDs = [2]: "HMDB0000001, HMDB0000002"
biodb.DEBUG[2024-04-13 16:05:54.580][private$doSearchForEntries] Total number of IDs = 2
biodb.TRACE[2024-04-13 16:05:54.582][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:54.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:54.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:54.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:54.585][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:54.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:54.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:54.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:54.589][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:54.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:54.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:54.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:54.592][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:54.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:54.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:54.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-13 16:05:54.596][private$doSearchForEntries] MATCHED = TRUE
biodb.DEBUG[2024-04-13 16:05:54.597][private$doSearchForEntries] COUNT IDS = 1
biodb.INFO [2024-04-13 16:05:54.609][biodb::testThat]
biodb.INFO [2024-04-13 16:05:54.610][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. ").
biodb.INFO [2024-04-13 16:05:54.611][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-13 16:05:54.611][biodb::testThat]
biodb.TRACE[2024-04-13 16:05:54.629][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-04-13 16:05:54.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-04-13 16:05:54.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:54.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:54.633][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-04-13 16:05:54.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-04-13 16:05:54.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:54.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:54.636][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-04-13 16:05:54.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-04-13 16:05:54.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:54.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:54.640][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-04-13 16:05:54.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-04-13 16:05:54.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:54.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:54.679][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-04-13 16:05:54.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-04-13 16:05:54.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:54.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:54.683][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-04-13 16:05:54.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-04-13 16:05:54.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:54.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:54.687][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-04-13 16:05:54.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-04-13 16:05:54.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:54.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:54.690][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-04-13 16:05:54.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-04-13 16:05:54.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:54.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-04-13 16:05:54.699][biodb::testThat]
biodb.INFO [2024-04-13 16:05:54.700][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-04-13 16:05:54.701][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-13 16:05:54.702][biodb::testThat]
biodb.INFO [2024-04-13 16:05:54.712][biodb::testThat]
biodb.INFO [2024-04-13 16:05:54.713][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-04-13 16:05:54.714][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-13 16:05:54.715][biodb::testThat]
biodb.INFO [2024-04-13 16:05:54.721][biodb::testThat]
biodb.INFO [2024-04-13 16:05:54.722][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. ").
biodb.INFO [2024-04-13 16:05:54.723][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-13 16:05:54.724][biodb::testThat]
biodb.DEBUG[2024-04-13 16:05:54.727][function(conn, opt)] Trying to download "http://www.hmdb.ca/metabolites/HMDB0000001".
biodb.DEBUG[2024-04-13 16:05:57.395][getUrlContent] Use RCurl for downloading content of URL http://www.hmdb.ca/metabolites/HMDB0000001.
biodb.INFO [2024-04-13 16:05:57.515][biodb::testThat]
biodb.INFO [2024-04-13 16:05:57.517][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. ").
biodb.INFO [2024-04-13 16:05:57.520][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-13 16:05:57.522][biodb::testThat]
biodb.DEBUG[2024-04-13 16:05:57.906][getUrlContent] Use RCurl for downloading content of URL http://www.hmdb.ca/structures/HMDB0000001/image.png.
biodb.TRACE[2024-04-13 16:05:57.933][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:57.935][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:57.955][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:57.957][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:57.959][ef$get] Asked field names are: description.
biodb.TRACE[2024-04-13 16:05:57.961][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-04-13 16:05:57.963][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:57.965][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:57.967][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-04-13 16:05:57.969][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-04-13 16:05:57.971][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:57.972][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:57.974][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-13 16:05:57.976][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-13 16:05:57.977][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:57.979][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:57.980][ef$get] Asked field names are: description.
biodb.TRACE[2024-04-13 16:05:57.982][ef$get] Realnames of fields are: description.
biodb.TRACE[2024-04-13 16:05:57.983][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:57.984][ef$get] fields variable is a list.
biodb.TRACE[2024-04-13 16:05:57.986][ef$get] Asked field names are: secondary.accessions.
biodb.TRACE[2024-04-13 16:05:57.987][ef$get] Realnames of fields are: secondary.accessions.
biodb.TRACE[2024-04-13 16:05:57.988][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-13 16:05:57.990][ef$get] fields variable is a list.
biodb.INFO [2024-04-13 16:05:57.991][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-04-13 16:05:57.992][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector hmdb.metabolites from the request scheduler
biodb.INFO [2024-04-13 16:05:57.994][self$deleteConn] Connector "hmdb.metabolites" deleted.
biodb.DEBUG[2024-04-13 16:05:57.995][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-04-13 16:05:57.996][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-13 16:05:57.997][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-13 16:05:57.998][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-13 16:05:57.999][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-13 16:05:58.000][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-04-13 16:05:58.001][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 147 ]
>
> proc.time()
user system elapsed
4.932 0.156 7.926
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbHmdb_1.8.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc-longtests/meat/biodbHmdb.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* 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 ‘1.8.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘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 ‘/home/biocbuild/bbs-3.18-bioc-longtests/meat/biodbHmdb.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* checking installed package size ... NOTE
installed size is 7.5Mb
sub-directories of 1Mb or more:
libs 7.0Mb
* 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... 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’
OK
* DONE
Status: 2 WARNINGs, 2 NOTEs
See
‘/home/biocbuild/bbs-3.18-bioc-longtests/meat/biodbHmdb.Rcheck/00check.log’
for details.
biodbHmdb.Rcheck/00install.out
* installing *source* package ‘biodbHmdb’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -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"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c FileEntryMaker.cpp -o FileEntryMaker.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c StringEnrtryMaker.cpp -o StringEnrtryMaker.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c TagDetector.cpp -o TagDetector.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c XmlSplitter.cpp -o XmlSplitter.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c extractXmlEntries.cpp -o extractXmlEntries.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c test-100-TagDetector.cpp -o test-100-TagDetector.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c test-150-StringEntryMaker.cpp -o test-150-StringEntryMaker.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c test-200-XmlSplitter.cpp -o test-200-XmlSplitter.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c test-runner.cpp -o test-runner.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.18-bioc/R/lib -L/usr/local/lib -o biodbHmdb.so 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 -L/home/biocbuild/bbs-3.18-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.18-bioc-longtests/meat/biodbHmdb.Rcheck/00LOCK-biodbHmdb/00new/biodbHmdb/libs
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (biodbHmdb)