| Back to Long Tests report for BioC 3.20 |
This page was generated on 2024-06-29 23:55 -0400 (Sat, 29 Jun 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4693 |
| palomino6 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4408 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" | 4407 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 11/32 | Hostname | OS / Arch | CHECK | |||||||
| biodbNci 1.9.0 (landing page) Pierrick Roger
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | |||||||
| palomino6 | Windows Server 2022 Datacenter / x64 | OK | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | ||||||||
|
To the developers/maintainers of the biodbNci package: - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: biodbNci |
| Version: 1.9.0 |
| Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNci_1.9.0.tar.gz |
| StartedAt: 2024-06-29 16:04:51 -0400 (Sat, 29 Jun 2024) |
| EndedAt: 2024-06-29 16:05:56 -0400 (Sat, 29 Jun 2024) |
| EllapsedTime: 65.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: biodbNci.Rcheck |
| Warnings: 0 |
biodbNci.Rcheck/tests/testthat.Rout
R version 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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(biodbNci)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbNci")
biodb.INFO [2024-06-29 16:05:52.440][biodb::testContext]
biodb.INFO [2024-06-29 16:05:52.442][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-29 16:05:52.443][biodb::testContext] Test context - Generic long tests
biodb.INFO [2024-06-29 16:05:52.444][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-29 16:05:52.445][biodb::testContext]
biodb.INFO [2024-06-29 16:05:52.451][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.13.0.
biodb.DEBUG[2024-06-29 16:05:52.453][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-06-29 16:05:52.460][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-29 16:05:52.461][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-06-29 16:05:52.462][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-06-29 16:05:52.462][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:52.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:52.464][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:52.465][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-06-29 16:05:52.481][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-06-29 16:05:52.482][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:52.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:52.484][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:52.485][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-06-29 16:05:52.486][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-06-29 16:05:52.486][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:52.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:52.488][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:52.489][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-06-29 16:05:52.490][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-06-29 16:05:52.491][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-06-29 16:05:52.491][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:52.492][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:52.493][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:52.494][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-06-29 16:05:52.495][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-06-29 16:05:52.496][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-06-29 16:05:52.496][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:52.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:52.498][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:52.499][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-06-29 16:05:52.500][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-06-29 16:05:52.501][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:52.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:52.502][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:52.503][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-06-29 16:05:52.504][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-06-29 16:05:52.505][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-06-29 16:05:52.506][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:52.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:52.507][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:52.508][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-06-29 16:05:52.509][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-06-29 16:05:52.510][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:52.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:52.511][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:52.512][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-06-29 16:05:52.513][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-06-29 16:05:52.514][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-06-29 16:05:52.515][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:52.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:52.516][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:52.517][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-06-29 16:05:52.518][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-06-29 16:05:52.519][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-06-29 16:05:52.520][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-06-29 16:05:52.521][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-06-29 16:05:52.522][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-06-29 16:05:52.523][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:52.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:52.524][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:52.525][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-06-29 16:05:52.526][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-06-29 16:05:52.527][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:52.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:52.528][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:52.529][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-06-29 16:05:52.530][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-06-29 16:05:52.531][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:52.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:52.532][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:52.533][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-06-29 16:05:52.534][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-06-29 16:05:52.535][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:52.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:52.537][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:52.537][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-06-29 16:05:52.538][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-06-29 16:05:52.539][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:52.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:52.541][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:52.542][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-06-29 16:05:52.542][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-06-29 16:05:52.543][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:52.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:52.545][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:52.546][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-06-29 16:05:52.547][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-06-29 16:05:52.551][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-06-29 16:05:52.552][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:52.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:52.553][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:52.554][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-06-29 16:05:52.555][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-06-29 16:05:52.556][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-06-29 16:05:52.557][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:52.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:52.558][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:52.562][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-06-29 16:05:52.598][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-29 16:05:52.612][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-06-29 16:05:52.613][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-29 16:05:52.614][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-29 16:05:52.615][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-29 16:05:52.616][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-29 16:05:52.617][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-29 16:05:52.617][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-29 16:05:52.618][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-29 16:05:52.619][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-29 16:05:52.620][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-29 16:05:52.621][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-06-29 16:05:52.622][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-29 16:05:52.623][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:05:52.624][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-29 16:05:52.625][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-29 16:05:52.625][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-29 16:05:52.625][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-29 16:05:52.625][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-29 16:05:52.625][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-29 16:05:52.625][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-29 16:05:52.626][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-29 16:05:52.627][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-29 16:05:52.628][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-29 16:05:52.629][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-29 16:05:52.630][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-29 16:05:52.630][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-29 16:05:52.631][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:05:52.632][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-29 16:05:52.633][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-29 16:05:52.634][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-29 16:05:52.635][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:05:52.636][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-06-29 16:05:52.637][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-29 16:05:52.638][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-06-29 16:05:52.639][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-29 16:05:52.640][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-29 16:05:52.641][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-29 16:05:52.642][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-29 16:05:52.643][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-29 16:05:52.643][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-29 16:05:52.644][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-29 16:05:52.645][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-29 16:05:52.646][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-29 16:05:52.647][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-06-29 16:05:52.648][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-29 16:05:52.649][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:05:52.650][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-29 16:05:52.650][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-29 16:05:52.650][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-29 16:05:52.650][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-29 16:05:52.650][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-29 16:05:52.650][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-29 16:05:52.651][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-29 16:05:52.652][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-29 16:05:52.653][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-29 16:05:52.654][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-29 16:05:52.655][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-29 16:05:52.656][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-29 16:05:52.656][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-29 16:05:52.657][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:05:52.658][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-29 16:05:52.659][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-29 16:05:52.660][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-29 16:05:52.661][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:05:52.662][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-06-29 16:05:52.663][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-29 16:05:52.664][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-06-29 16:05:52.665][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-29 16:05:52.666][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-29 16:05:52.667][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-29 16:05:52.668][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-29 16:05:52.669][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-29 16:05:52.670][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-29 16:05:52.670][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-29 16:05:52.671][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-29 16:05:52.672][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-29 16:05:52.673][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-06-29 16:05:52.674][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-29 16:05:52.675][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:05:52.676][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-29 16:05:52.677][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:05:52.677][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-29 16:05:52.678][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-29 16:05:52.679][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-29 16:05:52.680][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-29 16:05:52.681][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-29 16:05:52.682][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-29 16:05:52.682][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-29 16:05:52.683][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:05:52.684][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-29 16:05:52.685][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-29 16:05:52.686][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-29 16:05:52.687][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:05:52.688][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-06-29 16:05:52.689][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-29 16:05:52.690][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-06-29 16:05:52.691][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-29 16:05:52.692][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-29 16:05:52.693][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-29 16:05:52.694][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-29 16:05:52.695][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-29 16:05:52.695][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-29 16:05:52.696][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-29 16:05:52.697][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-29 16:05:52.698][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-29 16:05:52.699][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-06-29 16:05:52.700][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-29 16:05:52.701][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:05:52.702][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-29 16:05:52.702][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:05:52.703][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-29 16:05:52.704][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-29 16:05:52.705][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-29 16:05:52.706][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-29 16:05:52.707][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-29 16:05:52.708][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-29 16:05:52.708][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-29 16:05:52.709][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:05:52.710][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-29 16:05:52.711][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-29 16:05:52.712][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-29 16:05:52.713][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:05:52.716][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-29 16:05:52.717][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:52.718][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:52.719][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:52.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:05:52.720][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:05:52.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:52.722][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:52.723][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:52.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:05:52.724][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:05:52.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:52.726][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:52.727][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:52.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:05:52.728][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:05:52.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:52.730][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:52.731][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:52.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:05:52.732][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:05:52.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:52.734][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:52.735][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:52.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:05:52.736][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:05:52.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:52.738][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:52.738][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:52.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:05:52.740][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:05:52.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:52.742][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:52.742][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:52.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:05:52.744][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:05:52.745][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:52.746][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:52.750][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:52.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:05:52.752][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:05:52.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:52.753][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:52.754][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:52.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:05:52.756][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:05:52.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:52.757][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:52.758][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:52.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:05:52.759][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:05:52.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:52.761][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:52.762][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:52.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:05:52.763][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:05:52.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:52.765][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:52.766][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:52.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:05:52.767][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:05:52.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:52.769][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:52.769][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:52.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:05:52.771][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:05:52.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:52.773][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:52.773][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:52.774][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:05:52.775][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:05:52.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:52.777][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:52.777][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:52.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:05:52.779][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:05:52.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:52.781][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:52.781][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:52.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:05:52.783][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:05:52.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:52.784][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[2024-06-29 16:05:52.785][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:52.786][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:05:52.787][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:05:52.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:52.788][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:52.789][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-06-29 16:05:52.794][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-06-29 16:05:52.795][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-06-29 16:05:52.796][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-06-29 16:05:52.797][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-29 16:05:52.799][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-29 16:05:52.800][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-06-29 16:05:52.801][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-06-29 16:05:52.802][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-29 16:05:52.804][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-29 16:05:52.805][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-29 16:05:52.806][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-06-29 16:05:52.807][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-06-29 16:05:52.809][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-06-29 16:05:52.810][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-06-29 16:05:52.811][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-29 16:05:52.812][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-06-29 16:05:52.814][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-06-29 16:05:52.815][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-29 16:05:52.816][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-06-29 16:05:52.817][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-06-29 16:05:52.819][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-06-29 16:05:52.820][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-06-29 16:05:52.821][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-06-29 16:05:52.822][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-06-29 16:05:52.824][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-06-29 16:05:52.825][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-06-29 16:05:52.826][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-06-29 16:05:52.827][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-06-29 16:05:52.828][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-06-29 16:05:52.830][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-06-29 16:05:52.831][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-06-29 16:05:52.836][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-06-29 16:05:52.838][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-06-29 16:05:52.840][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-06-29 16:05:52.841][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-06-29 16:05:52.842][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-06-29 16:05:52.844][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-06-29 16:05:52.845][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-06-29 16:05:52.847][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-06-29 16:05:52.848][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-06-29 16:05:52.849][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-06-29 16:05:52.851][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-06-29 16:05:52.852][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-06-29 16:05:52.854][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-06-29 16:05:52.855][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-06-29 16:05:52.856][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-06-29 16:05:52.858][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-06-29 16:05:52.859][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-06-29 16:05:52.861][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-06-29 16:05:52.862][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-06-29 16:05:52.864][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-06-29 16:05:52.865][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-06-29 16:05:52.866][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-06-29 16:05:52.868][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-06-29 16:05:52.869][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-06-29 16:05:52.871][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-06-29 16:05:52.872][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-06-29 16:05:52.873][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-06-29 16:05:52.875][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-06-29 16:05:52.876][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-06-29 16:05:52.877][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-06-29 16:05:52.879][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-06-29 16:05:52.880][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-06-29 16:05:52.882][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-06-29 16:05:52.883][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-06-29 16:05:52.884][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-29 16:05:52.886][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-29 16:05:52.887][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-06-29 16:05:52.889][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-06-29 16:05:52.890][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-06-29 16:05:52.891][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-06-29 16:05:52.893][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-06-29 16:05:52.894][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-06-29 16:05:52.895][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-06-29 16:05:52.897][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-06-29 16:05:52.898][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-06-29 16:05:52.899][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-06-29 16:05:52.901][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-06-29 16:05:52.902][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-06-29 16:05:52.903][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-06-29 16:05:52.905][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-06-29 16:05:52.906][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-06-29 16:05:52.913][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-06-29 16:05:52.915][initialize] This is biodb version 1.13.0.
biodb.DEBUG[2024-06-29 16:05:52.918][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-29 16:05:52.919][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:05:52.920][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:05:52.921][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:52.935][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:52.939][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:52.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:05:52.941][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:05:52.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:05:52.943][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:05:52.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:52.945][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:52.946][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:52.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:05:52.947][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:05:52.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:05:52.949][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:05:52.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:52.951][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:52.952][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:52.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:05:52.953][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:05:52.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:05:52.955][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:05:52.956][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:52.957][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:52.958][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:52.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:05:52.959][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:05:52.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:05:52.961][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:05:52.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:52.963][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:52.964][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:52.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:05:52.966][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:05:52.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:05:52.967][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:05:52.968][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:52.969][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:52.970][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:52.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:05:52.972][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:05:52.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:05:52.973][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:05:52.974][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:52.975][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:52.976][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:52.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:05:52.978][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:05:52.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:05:52.979][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:05:52.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:52.981][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:52.982][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:52.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:05:52.984][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:05:52.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:05:52.985][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:05:52.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:52.987][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:52.988][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:52.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:05:52.990][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:05:52.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:05:52.991][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:05:52.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:52.993][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:52.994][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:52.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:05:52.995][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:05:52.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:05:52.997][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:05:52.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:52.999][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:53.000][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:53.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:05:53.001][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:05:53.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:05:53.003][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:05:53.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:53.005][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:53.006][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:53.006][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:05:53.007][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:05:53.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:05:53.009][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:05:53.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:53.011][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:53.011][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:53.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:05:53.013][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:05:53.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:05:53.015][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:05:53.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:53.016][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:53.017][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:53.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:05:53.019][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:05:53.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:05:53.021][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:05:53.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:53.022][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:53.023][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:53.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:05:53.024][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:05:53.025][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:05:53.026][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:05:53.027][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:53.028][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:53.028][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:53.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:05:53.030][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:05:53.031][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:05:53.031][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:05:53.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:53.033][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:53.034][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:53.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:05:53.035][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:05:53.036][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:05:53.037][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:05:53.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:53.039][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:53.040][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2024-06-29 16:05:53.049][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2024-06-29 16:05:53.051][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-29 16:05:53.052][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2024-06-29 16:05:53.053][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-29 16:05:53.053][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-29 16:05:53.054][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2024-06-29 16:05:53.055][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2024-06-29 16:05:53.056][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-06-29 16:05:53.057][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-29 16:05:53.058][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2024-06-29 16:05:53.059][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-29 16:05:53.060][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-29 16:05:53.061][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2024-06-29 16:05:53.062][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-29 16:05:53.062][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2024-06-29 16:05:53.062][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2024-06-29 16:05:53.062][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2024-06-29 16:05:53.062][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2024-06-29 16:05:53.062][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2024-06-29 16:05:53.062][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2024-06-29 16:05:53.062][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2024-06-29 16:05:53.063][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-06-29 16:05:53.064][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:05:53.065][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-06-29 16:05:53.066][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-29 16:05:53.067][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-29 16:05:53.068][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-29 16:05:53.069][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-29 16:05:53.069][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-29 16:05:53.070][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-29 16:05:53.071][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2024-06-29 16:05:53.071][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2024-06-29 16:05:53.071][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2024-06-29 16:05:53.071][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2024-06-29 16:05:53.072][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-29 16:05:53.073][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-29 16:05:53.074][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-06-29 16:05:53.075][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:05:53.080][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2024-06-29 16:05:53.102][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2024-06-29 16:05:53.108][super$initialize] Register connector nci.cactus with the request scheduler
biodb.DEBUG[2024-06-29 16:05:53.111][private$bdb$getRequestScheduler()$re ...] Register connector nci.cactus.
biodb.DEBUG[2024-06-29 16:05:53.115][private$addConnectorRules] Create new rule for URL "cactus.nci.nih.gov" of connector "nci.cactus".
biodb.DEBUG[2024-06-29 16:05:53.119][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-29 16:05:53.120][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-29 16:05:53.122][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-06-29 16:05:53.123][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-06-29 16:05:53.124][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-06-29 16:05:53.125][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2024-06-29 16:05:53.134][biodb::testThat]
biodb.INFO [2024-06-29 16:05:53.135][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value ").
biodb.INFO [2024-06-29 16:05:53.136][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-29 16:05:53.136][biodb::testThat]
biodb.TRACE[2024-06-29 16:05:53.140][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.20-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-749674-content.sdf".
biodb.DEBUG[2024-06-29 16:05:53.141][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2024-06-29 16:05:53.145][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2024-06-29 16:05:53.153][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-29 16:05:53.154][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:05:53.155][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:05:53.167][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:05:53.168][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:05:53.168][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:53.169][FUN] Functions in observer BiodbConfig: [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[2024-06-29 16:05:53.186][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:05:53.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:05:53.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.190][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:05:53.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:05:53.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.205][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-29 16:05:53.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-29 16:05:53.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.231][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-29 16:05:53.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-29 16:05:53.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.235][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-29 16:05:53.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-29 16:05:53.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.238][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-29 16:05:53.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-29 16:05:53.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.242][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-29 16:05:53.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-29 16:05:53.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.246][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-29 16:05:53.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-29 16:05:53.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.250][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-29 16:05:53.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-29 16:05:53.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.253][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-29 16:05:53.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-29 16:05:53.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.257][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-29 16:05:53.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-29 16:05:53.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.261][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-29 16:05:53.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-29 16:05:53.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.264][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:05:53.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:05:53.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.268][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-29 16:05:53.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-29 16:05:53.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.307][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:05:53.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:05:53.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.310][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:05:53.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:05:53.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.314][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:05:53.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:05:53.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.347][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:05:53.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:05:53.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.350][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:05:53.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:05:53.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.354][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:05:53.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:05:53.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-29 16:05:53.357][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 749674.
biodb.TRACE[2024-06-29 16:05:53.359][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-29 16:05:53.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-29 16:05:53.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.363][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-29 16:05:53.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-29 16:05:53.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.366][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-29 16:05:53.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-29 16:05:53.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.370][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-29 16:05:53.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-29 16:05:53.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.387][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:05:53.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:05:53.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.401][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-29 16:05:53.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-29 16:05:53.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.408][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:05:53.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:05:53.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.411][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:05:53.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:05:53.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.415][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:05:53.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:05:53.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.420][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:05:53.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:05:53.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.423][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:05:53.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:05:53.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.431][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:05:53.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:05:53.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.434][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-29 16:05:53.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-29 16:05:53.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.438][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-29 16:05:53.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-29 16:05:53.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.441][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-29 16:05:53.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-29 16:05:53.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.450][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:05:53.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:05:53.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.454][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:05:53.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:05:53.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.457][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:05:53.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:05:53.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.461][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:05:53.462][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:05:53.463][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.464][ef$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.464][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:05:53.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:05:53.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.475][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-29 16:05:53.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-29 16:05:53.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.478][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-29 16:05:53.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-29 16:05:53.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.482][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-29 16:05:53.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-29 16:05:53.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.485][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-29 16:05:53.486][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-29 16:05:53.487][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.488][ef$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.489][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-29 16:05:53.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-29 16:05:53.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.498][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-29 16:05:53.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-29 16:05:53.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.502][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-29 16:05:53.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-29 16:05:53.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.505][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-29 16:05:53.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-29 16:05:53.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.509][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-29 16:05:53.510][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-29 16:05:53.510][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.511][ef$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.512][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-29 16:05:53.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-29 16:05:53.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.522][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-29 16:05:53.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-29 16:05:53.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.525][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-29 16:05:53.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-29 16:05:53.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.529][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-29 16:05:53.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-29 16:05:53.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.532][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-29 16:05:53.533][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-29 16:05:53.534][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.535][ef$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.536][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-29 16:05:53.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-29 16:05:53.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.545][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-29 16:05:53.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-29 16:05:53.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.549][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-29 16:05:53.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-29 16:05:53.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.552][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-29 16:05:53.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-29 16:05:53.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.556][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-29 16:05:53.557][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-29 16:05:53.562][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.563][ef$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.564][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-29 16:05:53.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-29 16:05:53.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.573][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:05:53.574][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:05:53.575][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.575][ef$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.579][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-29 16:05:53.580][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-29 16:05:53.581][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.582][ef$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.585][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-29 16:05:53.586][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-29 16:05:53.587][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.588][ef$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.592][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-29 16:05:53.592][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-29 16:05:53.593][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.594][ef$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.598][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-29 16:05:53.599][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-29 16:05:53.600][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.600][ef$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.615][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.20-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-750690-content.sdf".
biodb.DEBUG[2024-06-29 16:05:53.647][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2024-06-29 16:05:53.648][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2024-06-29 16:05:53.649][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-29 16:05:53.650][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:05:53.651][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:05:53.654][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:05:53.655][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:05:53.656][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:53.657][FUN] Functions in observer BiodbConfig: [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[2024-06-29 16:05:53.665][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:05:53.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:05:53.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.668][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:05:53.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:05:53.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.691][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-29 16:05:53.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-29 16:05:53.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.695][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-29 16:05:53.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-29 16:05:53.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.699][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-29 16:05:53.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-29 16:05:53.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.702][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-29 16:05:53.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-29 16:05:53.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.706][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-29 16:05:53.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-29 16:05:53.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.709][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-29 16:05:53.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-29 16:05:53.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.713][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:05:53.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:05:53.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.717][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:05:53.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:05:53.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.721][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:05:53.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:05:53.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.724][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:05:53.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:05:53.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.728][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:05:53.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:05:53.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.731][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:05:53.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:05:53.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.735][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:05:53.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:05:53.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.739][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-29 16:05:53.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-29 16:05:53.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.742][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-29 16:05:53.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-29 16:05:53.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.746][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-29 16:05:53.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-29 16:05:53.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.750][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-29 16:05:53.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-29 16:05:53.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.754][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-29 16:05:53.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-29 16:05:53.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.757][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-29 16:05:53.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-29 16:05:53.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.761][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:05:53.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:05:53.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.765][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-29 16:05:53.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-29 16:05:53.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.768][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:05:53.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:05:53.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.772][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:05:53.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:05:53.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.775][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:05:53.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:05:53.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.779][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:05:53.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:05:53.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.782][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:05:53.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:05:53.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.786][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:05:53.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:05:53.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-29 16:05:53.789][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 750690.
biodb.TRACE[2024-06-29 16:05:53.811][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-29 16:05:53.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-29 16:05:53.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.814][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-29 16:05:53.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-29 16:05:53.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.818][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-29 16:05:53.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-29 16:05:53.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.821][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-29 16:05:53.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-29 16:05:53.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.825][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:05:53.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:05:53.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.832][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-29 16:05:53.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-29 16:05:53.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.838][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:05:53.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:05:53.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.842][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:05:53.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:05:53.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.845][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:05:53.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:05:53.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.850][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:05:53.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:05:53.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.853][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:05:53.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:05:53.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.857][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:05:53.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:05:53.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.861][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-29 16:05:53.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-29 16:05:53.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.864][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-29 16:05:53.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-29 16:05:53.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.868][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-29 16:05:53.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-29 16:05:53.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.884][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:05:53.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:05:53.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.888][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:05:53.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:05:53.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.891][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:05:53.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:05:53.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.895][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:05:53.896][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:05:53.897][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.898][ef$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.898][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:05:53.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:05:53.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.908][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-29 16:05:53.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-29 16:05:53.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.911][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-29 16:05:53.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-29 16:05:53.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.915][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-29 16:05:53.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-29 16:05:53.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.918][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-29 16:05:53.919][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-29 16:05:53.920][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.921][ef$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.922][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-29 16:05:53.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-29 16:05:53.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.935][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:05:53.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:05:53.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.938][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:05:53.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:05:53.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.942][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:05:53.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:05:53.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.945][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:05:53.946][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:05:53.947][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.948][ef$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.949][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:05:53.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:05:53.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.958][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-29 16:05:53.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-29 16:05:53.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.962][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-29 16:05:53.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-29 16:05:53.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.965][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-29 16:05:53.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-29 16:05:53.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.969][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-29 16:05:53.970][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-29 16:05:53.971][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.972][ef$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.972][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-29 16:05:53.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-29 16:05:53.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.982][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-29 16:05:53.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-29 16:05:53.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.985][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-29 16:05:53.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-29 16:05:53.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.989][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-29 16:05:53.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-29 16:05:53.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.992][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-29 16:05:53.993][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-29 16:05:53.994][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.995][ef$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:53.996][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-29 16:05:53.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-29 16:05:53.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:53.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:54.005][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-29 16:05:54.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-29 16:05:54.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:54.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:54.009][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-29 16:05:54.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-29 16:05:54.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:54.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:54.012][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-29 16:05:54.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-29 16:05:54.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:54.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:54.016][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-29 16:05:54.017][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-29 16:05:54.018][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:54.018][ef$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:54.019][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-29 16:05:54.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-29 16:05:54.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:54.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:54.029][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-29 16:05:54.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-29 16:05:54.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:54.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:54.032][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-29 16:05:54.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-29 16:05:54.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:54.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:54.036][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-29 16:05:54.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-29 16:05:54.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:54.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:54.039][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-29 16:05:54.040][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-29 16:05:54.041][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:54.042][ef$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:54.043][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-29 16:05:54.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-29 16:05:54.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:54.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:54.056][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:05:54.057][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:05:54.058][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:54.058][ef$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:54.062][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-29 16:05:54.063][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-29 16:05:54.064][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:54.064][ef$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:54.068][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-29 16:05:54.069][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-29 16:05:54.070][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:54.071][ef$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:54.074][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-29 16:05:54.075][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-29 16:05:54.076][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:54.077][ef$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:54.080][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-29 16:05:54.081][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-29 16:05:54.082][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:54.083][ef$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:54.087][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-29 16:05:54.088][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-29 16:05:54.088][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:54.089][ef$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:54.093][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:05:54.094][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:05:54.095][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:54.096][ef$get] fields variable is a list.
biodb.INFO [2024-06-29 16:05:54.102][biodb::testThat]
biodb.INFO [2024-06-29 16:05:54.102][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-06-29 16:05:54.103][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-29 16:05:54.104][biodb::testThat]
biodb.DEBUG[2024-06-29 16:05:54.106][private$loadEntries] Creating entries from ids [2]: "749674, 750690".
biodb.DEBUG[2024-06-29 16:05:54.113][conn$getEntryContent] Get NCI CACTUS entry content(s) for 2 id(s)...
biodb.DEBUG[2024-06-29 16:05:54.117][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2024-06-29 16:05:54.118][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.TRACE[2024-06-29 16:05:54.120][cch$loadFileContent] Trying to load 2 files from cache: [2]: "749674, 750690".
biodb.TRACE[2024-06-29 16:05:54.121][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2024-06-29 16:05:54.123][loadFileContents] Loaded 2 files from cache: [2]: "/home/biocbuild/.cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/749674.sdf, /home/biocbuild/.cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/750690.sdf".
biodb.DEBUG[2024-06-29 16:05:54.124][conn$getEntryContent] 2 NCI CACTUS entry content(s) loaded from cache.
biodb.DEBUG[2024-06-29 16:05:54.125][self$createEntryFromContent] Creating NCI CACTUS entries from 2 content(s).
biodb.DEBUG[2024-06-29 16:05:54.126][self$createEntryFromContent] Parsing 2 NCI CACTUS entries.
biodb.DEBUG[2024-06-29 16:05:54.127][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-29 16:05:54.128][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:05:54.129][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:05:54.132][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:05:54.133][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:05:54.134][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:54.135][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-29 16:05:54.141][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:05:54.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:05:54.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:54.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:54.144][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:05:54.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:05:54.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:54.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:54.149][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-29 16:05:54.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-29 16:05:54.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:54.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:54.152][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-29 16:05:54.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-29 16:05:54.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:54.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:54.156][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-29 16:05:54.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-29 16:05:54.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:54.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:54.160][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-29 16:05:54.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-29 16:05:54.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:54.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:54.164][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-29 16:05:54.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-29 16:05:54.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:54.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:54.168][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-29 16:05:54.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-29 16:05:54.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:54.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:54.171][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-29 16:05:54.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-29 16:05:54.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:54.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:54.175][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-29 16:05:54.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-29 16:05:54.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:54.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:54.179][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-29 16:05:54.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-29 16:05:54.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:54.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:54.183][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-29 16:05:54.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-29 16:05:54.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:54.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:54.190][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:05:54.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:05:54.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:54.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:54.194][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-29 16:05:54.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-29 16:05:54.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:54.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:54.197][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:05:54.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:05:54.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:54.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:54.201][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:05:54.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:05:54.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:54.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:54.204][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:05:54.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:05:54.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:54.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-29 16:05:54.208][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-29 16:05:54.209][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:05:54.209][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:05:54.213][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:05:54.214][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:05:54.215][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:54.216][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-29 16:05:54.224][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:05:54.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:05:54.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:54.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:54.227][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:05:54.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:05:54.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:54.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:54.232][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-29 16:05:54.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-29 16:05:54.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:54.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:54.235][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-29 16:05:54.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-29 16:05:54.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:54.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:54.239][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-29 16:05:54.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-29 16:05:54.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:54.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:54.243][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-29 16:05:54.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-29 16:05:54.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:54.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:54.247][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-29 16:05:54.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-29 16:05:54.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:54.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:54.250][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-29 16:05:54.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-29 16:05:54.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:54.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:54.254][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:05:54.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:05:54.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:54.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:54.257][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:05:54.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:05:54.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:54.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:54.261][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:05:54.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:05:54.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:54.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:54.265][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:05:54.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:05:54.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:54.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:54.268][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:05:54.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:05:54.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:54.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:54.272][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:05:54.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:05:54.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:54.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:54.275][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:05:54.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:05:54.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:54.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:54.279][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-29 16:05:54.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-29 16:05:54.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:54.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:54.283][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-29 16:05:54.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-29 16:05:54.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:54.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:54.287][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-29 16:05:54.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-29 16:05:54.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:54.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:54.290][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-29 16:05:54.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-29 16:05:54.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:54.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:54.295][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-29 16:05:54.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-29 16:05:54.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:54.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:54.298][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-29 16:05:54.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-29 16:05:54.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:54.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:54.302][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:05:54.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:05:54.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:54.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:54.305][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-29 16:05:54.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-29 16:05:54.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:54.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:54.309][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:05:54.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:05:54.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:54.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:54.312][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:05:54.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:05:54.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:54.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:54.319][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:05:54.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:05:54.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:54.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:54.323][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:05:54.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:05:54.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:54.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:54.326][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:05:54.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:05:54.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:54.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:54.330][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:05:54.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:05:54.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:54.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:54.333][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:05:54.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:05:54.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:54.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:54.337][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:05:54.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:05:54.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:54.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:54.340][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:05:54.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:05:54.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:54.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-29 16:05:54.344][self$createEntryFromContent] Accession numbers: 749674, 750690.
biodb.TRACE[2024-06-29 16:05:54.345][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-06-29 16:05:54.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-06-29 16:05:54.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:54.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:54.348][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-06-29 16:05:54.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-06-29 16:05:54.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:54.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:54.352][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-06-29 16:05:54.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-06-29 16:05:54.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:54.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:54.359][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-06-29 16:05:54.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-06-29 16:05:54.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:54.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:54.362][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-06-29 16:05:54.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-06-29 16:05:54.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:54.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:54.366][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-06-29 16:05:54.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-06-29 16:05:54.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:54.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-29 16:05:54.375][biodb::testThat]
biodb.INFO [2024-06-29 16:05:54.375][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field ").
biodb.INFO [2024-06-29 16:05:54.376][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-29 16:05:54.377][biodb::testThat]
biodb.INFO [2024-06-29 16:05:54.382][biodb::testThat]
biodb.INFO [2024-06-29 16:05:54.383][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. ").
biodb.INFO [2024-06-29 16:05:54.384][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-29 16:05:54.385][biodb::testThat]
biodb.WARN [2024-06-29 16:05:54.403][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2024-06-29 16:05:54.421][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2024-06-29 16:05:54.428][biodb::testThat]
biodb.INFO [2024-06-29 16:05:54.429][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. ").
biodb.INFO [2024-06-29 16:05:54.430][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-29 16:05:54.431][biodb::testThat]
biodb.TRACE[2024-06-29 16:05:54.455][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-29 16:05:54.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-29 16:05:54.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:54.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:54.458][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-29 16:05:54.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-29 16:05:54.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:54.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:54.462][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-29 16:05:54.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-29 16:05:54.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:54.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:54.466][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-29 16:05:54.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-29 16:05:54.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:54.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:54.498][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-29 16:05:54.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-29 16:05:54.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:54.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:54.501][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-29 16:05:54.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-29 16:05:54.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:54.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:54.505][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-29 16:05:54.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-29 16:05:54.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:54.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:05:54.509][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-29 16:05:54.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-29 16:05:54.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:05:54.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-29 16:05:54.516][biodb::testThat]
biodb.INFO [2024-06-29 16:05:54.517][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-06-29 16:05:54.518][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-29 16:05:54.519][biodb::testThat]
biodb.INFO [2024-06-29 16:05:54.524][biodb::testThat]
biodb.INFO [2024-06-29 16:05:54.525][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-06-29 16:05:54.526][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-29 16:05:54.527][biodb::testThat]
biodb.INFO [2024-06-29 16:05:54.533][biodb::testThat]
biodb.INFO [2024-06-29 16:05:54.534][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. ").
biodb.INFO [2024-06-29 16:05:54.534][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-29 16:05:54.535][biodb::testThat]
biodb.INFO [2024-06-29 16:05:54.540][biodb::testThat]
biodb.INFO [2024-06-29 16:05:54.541][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. ").
biodb.INFO [2024-06-29 16:05:54.542][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-29 16:05:54.543][biodb::testThat]
biodb.INFO [2024-06-29 16:05:54.547][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-06-29 16:05:54.552][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector nci.cactus from the request scheduler
biodb.INFO [2024-06-29 16:05:54.553][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2024-06-29 16:05:54.554][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-06-29 16:05:54.555][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:05:54.555][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:05:54.556][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:05:54.557][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:05:54.558][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:54.559][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-06-29 16:05:54.567][biodb::testContext]
biodb.INFO [2024-06-29 16:05:54.567][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-29 16:05:54.568][biodb::testContext] Test context - Example long tests
biodb.INFO [2024-06-29 16:05:54.569][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-29 16:05:54.570][biodb::testContext]
biodb.INFO [2024-06-29 16:05:54.572][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.13.0.
biodb.DEBUG[2024-06-29 16:05:54.573][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-06-29 16:05:54.577][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-29 16:05:54.578][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-06-29 16:05:54.579][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-06-29 16:05:54.579][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:54.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:54.581][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:54.582][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-06-29 16:05:54.583][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-06-29 16:05:54.583][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:54.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:54.585][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:54.586][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-06-29 16:05:54.587][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-06-29 16:05:54.588][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:54.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:54.589][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:54.590][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-06-29 16:05:54.591][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-06-29 16:05:54.592][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-06-29 16:05:54.593][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:54.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:54.594][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:54.595][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-06-29 16:05:54.596][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-06-29 16:05:54.597][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-06-29 16:05:54.598][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:54.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:54.599][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:54.600][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-06-29 16:05:54.601][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-06-29 16:05:54.602][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:54.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:54.604][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:54.604][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-06-29 16:05:54.605][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-06-29 16:05:54.606][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-06-29 16:05:54.607][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:54.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:54.609][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:54.609][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-06-29 16:05:54.610][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-06-29 16:05:54.611][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:54.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:54.613][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:54.614][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-06-29 16:05:54.615][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-06-29 16:05:54.615][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-06-29 16:05:54.616][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:54.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:54.618][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:54.619][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-06-29 16:05:54.620][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-06-29 16:05:54.620][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-06-29 16:05:54.621][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-06-29 16:05:54.622][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-06-29 16:05:54.623][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-06-29 16:05:54.624][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:54.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:54.626][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:54.626][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-06-29 16:05:54.627][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-06-29 16:05:54.628][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:54.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:54.630][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:54.631][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-06-29 16:05:54.632][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-06-29 16:05:54.632][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:54.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:54.634][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:54.635][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-06-29 16:05:54.636][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-06-29 16:05:54.637][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:54.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:54.638][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:54.639][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-06-29 16:05:54.640][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-06-29 16:05:54.641][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:54.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:54.642][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:54.643][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-06-29 16:05:54.644][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-06-29 16:05:54.645][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:54.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:54.646][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:54.647][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-06-29 16:05:54.648][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-06-29 16:05:54.652][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-06-29 16:05:54.653][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:54.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:54.654][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:54.655][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-06-29 16:05:54.656][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-06-29 16:05:54.657][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-06-29 16:05:54.658][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:54.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:54.659][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:54.660][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-06-29 16:05:54.662][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-29 16:05:54.663][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-06-29 16:05:54.664][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-29 16:05:54.665][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-29 16:05:54.666][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-29 16:05:54.667][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-29 16:05:54.667][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-29 16:05:54.668][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-29 16:05:54.669][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-29 16:05:54.670][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-29 16:05:54.671][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-29 16:05:54.672][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-06-29 16:05:54.673][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-29 16:05:54.674][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:05:54.679][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-29 16:05:54.680][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-29 16:05:54.680][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-29 16:05:54.680][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-29 16:05:54.680][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-29 16:05:54.680][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-29 16:05:54.681][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-29 16:05:54.681][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-29 16:05:54.682][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-29 16:05:54.683][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-29 16:05:54.684][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-29 16:05:54.685][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-29 16:05:54.686][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-29 16:05:54.686][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:05:54.687][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-29 16:05:54.688][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-29 16:05:54.689][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-29 16:05:54.690][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:05:54.691][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-06-29 16:05:54.692][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-29 16:05:54.693][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-06-29 16:05:54.694][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-29 16:05:54.695][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-29 16:05:54.696][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-29 16:05:54.697][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-29 16:05:54.698][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-29 16:05:54.699][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-29 16:05:54.700][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-29 16:05:54.701][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-29 16:05:54.701][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-29 16:05:54.702][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-06-29 16:05:54.703][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-29 16:05:54.704][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:05:54.705][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-29 16:05:54.706][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-29 16:05:54.706][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-29 16:05:54.706][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-29 16:05:54.706][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-29 16:05:54.706][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-29 16:05:54.707][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-29 16:05:54.708][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-29 16:05:54.709][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-29 16:05:54.709][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-29 16:05:54.710][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-29 16:05:54.711][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-29 16:05:54.712][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-29 16:05:54.713][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:05:54.714][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-29 16:05:54.714][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-29 16:05:54.715][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-29 16:05:54.716][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:05:54.717][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-06-29 16:05:54.719][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-29 16:05:54.720][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-06-29 16:05:54.721][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-29 16:05:54.722][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-29 16:05:54.722][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-29 16:05:54.723][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-29 16:05:54.724][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-29 16:05:54.725][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-29 16:05:54.726][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-29 16:05:54.727][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-29 16:05:54.728][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-29 16:05:54.729][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-06-29 16:05:54.729][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-29 16:05:54.730][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:05:54.731][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-29 16:05:54.732][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:05:54.733][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-29 16:05:54.734][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-29 16:05:54.735][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-29 16:05:54.736][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-29 16:05:54.736][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-29 16:05:54.737][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-29 16:05:54.738][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-29 16:05:54.739][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:05:54.740][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-29 16:05:54.741][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-29 16:05:54.741][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-29 16:05:54.742][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:05:54.743][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-06-29 16:05:54.745][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-29 16:05:54.746][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-06-29 16:05:54.747][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-29 16:05:54.747][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-29 16:05:54.748][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-29 16:05:54.749][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-29 16:05:54.750][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-29 16:05:54.751][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-29 16:05:54.752][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-29 16:05:54.753][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-29 16:05:54.754][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-29 16:05:54.755][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-06-29 16:05:54.755][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-29 16:05:54.756][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:05:54.757][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-29 16:05:54.758][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:05:54.759][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-29 16:05:54.760][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-29 16:05:54.761][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-29 16:05:54.761][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-29 16:05:54.762][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-29 16:05:54.763][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-29 16:05:54.764][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-29 16:05:54.765][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:05:54.766][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-29 16:05:54.766][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-29 16:05:54.767][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-29 16:05:54.768][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:05:54.769][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-29 16:05:54.770][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:54.771][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:54.772][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:54.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:05:54.773][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:05:54.774][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:54.775][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:54.776][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:54.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:05:54.777][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:05:54.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:54.779][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:54.780][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:54.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:05:54.781][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:05:54.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:54.783][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:54.784][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:54.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:05:54.785][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:05:54.786][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:54.787][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:54.788][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:54.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:05:54.789][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:05:54.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:54.791][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:54.792][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:54.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:05:54.793][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:05:54.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:54.795][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:54.796][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:54.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:05:54.801][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:05:54.802][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:54.802][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:54.803][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:54.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:05:54.805][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:05:54.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:54.806][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:54.807][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:54.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:05:54.809][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:05:54.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:54.810][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:54.811][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:54.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:05:54.813][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:05:54.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:54.814][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:54.815][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:54.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:05:54.816][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:05:54.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:54.818][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[2024-06-29 16:05:54.819][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:54.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:05:54.820][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:05:54.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:54.822][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:54.823][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:54.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:05:54.824][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:05:54.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:54.826][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:54.827][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:54.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:05:54.828][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:05:54.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:54.830][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:54.831][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:54.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:05:54.832][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:05:54.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:54.834][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:54.835][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:54.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:05:54.836][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:05:54.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:54.838][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:54.839][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:54.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:05:54.840][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:05:54.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:54.842][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:54.843][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-06-29 16:05:54.844][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-06-29 16:05:54.845][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-06-29 16:05:54.846][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-06-29 16:05:54.848][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-29 16:05:54.849][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-29 16:05:54.850][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-06-29 16:05:54.851][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-06-29 16:05:54.853][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-29 16:05:54.854][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-29 16:05:54.855][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-29 16:05:54.856][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-06-29 16:05:54.858][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-06-29 16:05:54.859][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-06-29 16:05:54.860][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-06-29 16:05:54.861][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-29 16:05:54.863][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-06-29 16:05:54.864][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-06-29 16:05:54.865][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-29 16:05:54.866][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-06-29 16:05:54.868][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-06-29 16:05:54.869][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-06-29 16:05:54.870][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-06-29 16:05:54.871][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-06-29 16:05:54.873][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-06-29 16:05:54.874][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-06-29 16:05:54.875][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-06-29 16:05:54.876][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-06-29 16:05:54.878][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-06-29 16:05:54.879][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-06-29 16:05:54.880][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-06-29 16:05:54.881][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-06-29 16:05:54.883][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-06-29 16:05:54.884][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-06-29 16:05:54.885][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-06-29 16:05:54.886][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-06-29 16:05:54.887][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-06-29 16:05:54.889][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-06-29 16:05:54.890][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-06-29 16:05:54.891][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-06-29 16:05:54.892][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-06-29 16:05:54.894][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-06-29 16:05:54.895][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-06-29 16:05:54.896][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-06-29 16:05:54.897][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-06-29 16:05:54.899][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-06-29 16:05:54.900][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-06-29 16:05:54.901][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-06-29 16:05:54.902][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-06-29 16:05:54.904][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-06-29 16:05:54.905][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-06-29 16:05:54.906][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-06-29 16:05:54.907][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-06-29 16:05:54.909][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-06-29 16:05:54.910][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-06-29 16:05:54.911][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-06-29 16:05:54.912][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-06-29 16:05:54.914][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-06-29 16:05:54.919][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-06-29 16:05:54.920][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-06-29 16:05:54.921][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-06-29 16:05:54.923][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-06-29 16:05:54.924][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-06-29 16:05:54.925][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-06-29 16:05:54.926][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-06-29 16:05:54.927][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-06-29 16:05:54.929][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-29 16:05:54.930][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-29 16:05:54.931][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-06-29 16:05:54.932][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-06-29 16:05:54.933][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-06-29 16:05:54.935][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-06-29 16:05:54.936][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-06-29 16:05:54.937][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-06-29 16:05:54.938][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-06-29 16:05:54.940][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-06-29 16:05:54.941][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-06-29 16:05:54.942][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-06-29 16:05:54.943][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-06-29 16:05:54.945][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-06-29 16:05:54.946][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-06-29 16:05:54.947][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-06-29 16:05:54.948][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-06-29 16:05:54.954][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-06-29 16:05:54.955][initialize] This is biodb version 1.13.0.
biodb.DEBUG[2024-06-29 16:05:54.956][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-29 16:05:54.957][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:05:54.958][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:05:54.958][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:54.959][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:54.960][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:54.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:05:54.962][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:05:54.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:05:54.963][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:05:54.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:54.965][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:54.966][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:54.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:05:54.967][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:05:54.968][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:05:54.969][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:05:54.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:54.970][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:54.971][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:54.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:05:54.973][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:05:54.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:05:54.974][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:05:54.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:54.976][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:54.977][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:54.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:05:54.978][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:05:54.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:05:54.980][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:05:54.981][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:54.981][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:54.982][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:54.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:05:54.984][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:05:54.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:05:54.985][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:05:54.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:54.987][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:54.988][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:54.988][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:05:54.989][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:05:54.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:05:54.991][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:05:54.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:54.992][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:54.993][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:54.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:05:54.995][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:05:54.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:05:54.996][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:05:54.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:54.998][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:54.999][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:54.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:05:55.000][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:05:55.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:05:55.002][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:05:55.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:55.003][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:55.004][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:55.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:05:55.006][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:05:55.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:05:55.007][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:05:55.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:55.009][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:55.010][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:55.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:05:55.011][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:05:55.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:05:55.013][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:05:55.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:55.015][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:55.015][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:55.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:05:55.017][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:05:55.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:05:55.018][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:05:55.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:55.020][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:55.021][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:55.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:05:55.022][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:05:55.023][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:05:55.024][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:05:55.025][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:55.026][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:55.026][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:55.027][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:05:55.028][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:05:55.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:05:55.029][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:05:55.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:55.031][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:55.032][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:55.033][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:05:55.037][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:05:55.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:05:55.039][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:05:55.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:55.041][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:55.041][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:55.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:05:55.043][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:05:55.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:05:55.044][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:05:55.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:55.046][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:55.047][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:55.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:05:55.048][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:05:55.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:05:55.050][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:05:55.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:55.051][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:55.052][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:05:55.053][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:05:55.054][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:05:55.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:05:55.055][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:05:55.056][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:55.057][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:05:55.058][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2024-06-29 16:05:55.060][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2024-06-29 16:05:55.061][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-29 16:05:55.062][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2024-06-29 16:05:55.063][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-29 16:05:55.064][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-29 16:05:55.065][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2024-06-29 16:05:55.066][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2024-06-29 16:05:55.067][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-06-29 16:05:55.068][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-29 16:05:55.069][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2024-06-29 16:05:55.069][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-29 16:05:55.070][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-29 16:05:55.071][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2024-06-29 16:05:55.072][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-29 16:05:55.073][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2024-06-29 16:05:55.073][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2024-06-29 16:05:55.073][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2024-06-29 16:05:55.073][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2024-06-29 16:05:55.073][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2024-06-29 16:05:55.073][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2024-06-29 16:05:55.073][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2024-06-29 16:05:55.074][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-06-29 16:05:55.075][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:05:55.076][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-06-29 16:05:55.077][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-29 16:05:55.077][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-29 16:05:55.078][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-29 16:05:55.079][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-29 16:05:55.080][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-29 16:05:55.081][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-29 16:05:55.082][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2024-06-29 16:05:55.082][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2024-06-29 16:05:55.082][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2024-06-29 16:05:55.082][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2024-06-29 16:05:55.083][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-29 16:05:55.083][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-29 16:05:55.084][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-06-29 16:05:55.085][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:05:55.086][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2024-06-29 16:05:55.089][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2024-06-29 16:05:55.090][super$initialize] Register connector nci.cactus with the request scheduler
biodb.DEBUG[2024-06-29 16:05:55.091][private$bdb$getRequestScheduler()$re ...] Register connector nci.cactus.
biodb.DEBUG[2024-06-29 16:05:55.092][private$addConnectorRules] Create new rule for URL "cactus.nci.nih.gov" of connector "nci.cactus".
biodb.DEBUG[2024-06-29 16:05:55.093][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-29 16:05:55.094][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-29 16:05:55.095][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-06-29 16:05:55.096][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-06-29 16:05:55.098][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-06-29 16:05:55.098][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2024-06-29 16:05:55.099][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-06-29 16:05:55.100][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector nci.cactus from the request scheduler
biodb.INFO [2024-06-29 16:05:55.101][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2024-06-29 16:05:55.102][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-06-29 16:05:55.103][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:05:55.104][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:05:55.104][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:05:55.105][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:05:55.106][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:05:55.107][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".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 92 ]
>
> proc.time()
user system elapsed
4.155 0.165 4.307
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNci_1.9.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.20-bioc-longtests/meat/biodbNci.Rcheck’
* using R version 4.4.0 RC (2024-04-16 r86468)
* using platform: x86_64-pc-linux-gnu
* 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 ‘biodbNci/DESCRIPTION’ ... OK
* this is package ‘biodbNci’ version ‘1.9.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbNci’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* checking installed package size ... NOTE
installed size is 6.3Mb
sub-directories of 1Mb or more:
libs 6.1Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... SKIPPED
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
Running ‘testthat.R’
OK
* DONE
Status: 1 NOTE
See
‘/home/biocbuild/bbs-3.20-bioc-longtests/meat/biodbNci.Rcheck/00check.log’
for details.
biodbNci.Rcheck/00install.out
* installing *source* package ‘biodbNci’ ... ** 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-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c extractEntries.cpp -o extractEntries.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c test-100-example.cpp -o test-100-example.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c test-runner.cpp -o test-runner.o g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o biodbNci.so RcppExports.o extractEntries.o test-100-example.o test-runner.o -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.20-bioc-longtests/meat/biodbNci.Rcheck/00LOCK-biodbNci/00new/biodbNci/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (biodbNci)