Pierrick Roger
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/biodb |
| git_branch: RELEASE_3_13 |
| git_last_commit: 84b7aff |
| git_last_commit_date: 2021-06-09 04:23:12 -0400 (Wed, 09 Jun 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:05:36 -0400 (Fri, 15 Oct 2021).
|
To the developers/maintainers of the biodb package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/biodb.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 178/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| biodb 1.0.4 (landing page) Pierrick Roger
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: biodb |
| Version: 1.0.4 |
| Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:biodb.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings biodb_1.0.4.tar.gz |
| StartedAt: 2021-10-14 09:02:35 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 09:05:57 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 201.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: biodb.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:biodb.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings biodb_1.0.4.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/biodb.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biodb/DESCRIPTION’ ... OK
* this is package ‘biodb’ version ‘1.0.4’
* 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 ‘biodb’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 6.3Mb
sub-directories of 1Mb or more:
R 1.8Mb
libs 3.8Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking 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 ... OK
* 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 ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/home/biocbuild/bbs-3.13-bioc/meat/biodb.Rcheck/00check.log’
for details.
biodb.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL biodb ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’ * installing *source* package ‘biodb’ ... ** using staged installation ** libs g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c closeMatchPpm.cpp -o closeMatchPpm.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c test-100-ms_matching.cpp -o test-100-ms_matching.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.13-bioc/R/library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c test-runner.cpp -o test-runner.o g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.13-bioc/R/lib -L/usr/local/lib -o biodb.so RcppExports.o closeMatchPpm.o test-100-ms_matching.o test-runner.o -L/home/biocbuild/bbs-3.13-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.13-bioc/R/library/00LOCK-biodb/00new/biodb/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 (biodb)
biodb.Rcheck/tests/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # vi: fdm=marker
> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodb)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> test_check("biodb")
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 1386 ]
>
> proc.time()
user system elapsed
116.020 4.381 121.120
biodb.Rcheck/biodb-Ex.timings
| name | user | system | elapsed | |
| BiodbCompounddbConn-class | 1.805 | 0.158 | 1.967 | |
| BiodbConfig-class | 0.372 | 0.001 | 0.373 | |
| BiodbConn-class | 0.439 | 0.005 | 0.445 | |
| BiodbConnBase-class | 0.359 | 0.002 | 0.360 | |
| BiodbCsvEntry-class | 0.036 | 0.004 | 0.039 | |
| BiodbDbInfo-class | 0.349 | 0.000 | 0.349 | |
| BiodbDbsInfo-class | 0.418 | 0.000 | 0.418 | |
| BiodbDownloadable-class | 0.075 | 0.000 | 0.075 | |
| BiodbEditable-class | 0.472 | 0.004 | 0.476 | |
| BiodbEntry-class | 0.635 | 0.008 | 0.642 | |
| BiodbEntryField-class | 0.39 | 0.00 | 0.39 | |
| BiodbEntryFields-class | 0.401 | 0.000 | 0.401 | |
| BiodbFactory-class | 0.498 | 0.000 | 0.498 | |
| BiodbHtmlEntry-class | 0.01 | 0.00 | 0.01 | |
| BiodbJsonEntry-class | 0.005 | 0.004 | 0.008 | |
| BiodbListEntry-class | 0.009 | 0.000 | 0.009 | |
| BiodbMain-class | 0.380 | 0.001 | 0.383 | |
| BiodbMassdbConn-class | 0.381 | 0.000 | 0.380 | |
| BiodbObserver-class | 0.396 | 0.005 | 0.402 | |
| BiodbPersistentCache-class | 1.693 | 0.174 | 1.867 | |
| BiodbRemotedbConn-class | 0.678 | 0.032 | 0.710 | |
| BiodbRequest | 0.557 | 0.014 | 1.552 | |
| BiodbRequestScheduler-class | 0.547 | 0.004 | 1.468 | |
| BiodbSdfEntry-class | 0.012 | 0.000 | 0.012 | |
| BiodbTestMsgAck-class | 0.409 | 0.002 | 0.411 | |
| BiodbTxtEntry-class | 0.019 | 0.000 | 0.019 | |
| BiodbUrl | 0.001 | 0.000 | 0.001 | |
| BiodbWritable-class | 0.682 | 0.000 | 0.682 | |
| BiodbXmlEntry-class | 0.012 | 0.000 | 0.012 | |
| CompCsvFileConn-class | 0.504 | 0.001 | 0.505 | |
| CompCsvFileEntry-class | 0.596 | 0.002 | 0.597 | |
| CompSqliteConn-class | 0.615 | 0.006 | 0.622 | |
| CompSqliteEntry-class | 0.482 | 0.000 | 0.482 | |
| CsvFileConn-class | 0.632 | 0.004 | 0.635 | |
| ExtConnClass | 0.188 | 0.004 | 0.193 | |
| ExtCpp | 0.287 | 0.012 | 0.300 | |
| ExtDefinitions | 0.079 | 0.004 | 0.082 | |
| ExtDescriptionFile | 0.060 | 0.000 | 0.061 | |
| ExtEntryClass | 0.057 | 0.000 | 0.058 | |
| ExtFileGenerator | 0.08 | 0.00 | 0.08 | |
| ExtGenerator | 1.268 | 0.008 | 1.279 | |
| ExtGitignore | 0.054 | 0.000 | 0.053 | |
| ExtLicense | 0.078 | 0.000 | 0.078 | |
| ExtMakefile | 0.079 | 0.000 | 0.079 | |
| ExtPackage | 1.624 | 0.036 | 1.660 | |
| ExtPackageFile | 0.054 | 0.004 | 0.059 | |
| ExtRbuildignore | 0.053 | 0.000 | 0.053 | |
| ExtReadme | 0.047 | 0.004 | 0.050 | |
| ExtTests | 0.442 | 0.004 | 0.447 | |
| ExtTravisFile | 0.049 | 0.004 | 0.053 | |
| ExtVignette | 0.047 | 0.004 | 0.050 | |
| MassCsvFileConn-class | 0.613 | 0.000 | 0.613 | |
| MassCsvFileEntry-class | 0.591 | 0.005 | 0.595 | |
| MassSqliteConn-class | 0.354 | 0.005 | 0.359 | |
| MassSqliteEntry-class | 0.371 | 0.002 | 0.373 | |
| Progress | 0.005 | 0.000 | 0.005 | |
| Range | 0.049 | 0.004 | 0.051 | |
| SqliteConn-class | 0.372 | 0.001 | 0.373 | |
| createBiodbTestInstance | 0.314 | 0.002 | 0.315 | |
| df2str | 0.001 | 0.000 | 0.002 | |
| error | 0.001 | 0.000 | 0.002 | |
| error0 | 0.001 | 0.000 | 0.002 | |
| genNewExtPkg | 1.289 | 0.004 | 1.293 | |
| getConnClassName | 0 | 0 | 0 | |
| getConnTypes | 0.001 | 0.000 | 0.000 | |
| getEntryClassName | 0.001 | 0.000 | 0.000 | |
| getEntryTypes | 0 | 0 | 0 | |
| getLicenses | 0.000 | 0.000 | 0.001 | |
| getLogger | 0.004 | 0.000 | 0.005 | |
| getPkgName | 0.000 | 0.000 | 0.001 | |
| getReposName | 0 | 0 | 0 | |
| getTestOutputDir | 0.000 | 0.001 | 0.000 | |
| listTestRefEntries | 0.000 | 0.001 | 0.001 | |
| logDebug | 0.000 | 0.000 | 0.001 | |
| logDebug0 | 0.000 | 0.000 | 0.001 | |
| logInfo | 0.001 | 0.000 | 0.002 | |
| logInfo0 | 0.001 | 0.000 | 0.002 | |
| logTrace | 0.000 | 0.000 | 0.001 | |
| logTrace0 | 0.000 | 0.000 | 0.001 | |
| lst2str | 0 | 0 | 0 | |
| newInst | 0.427 | 0.001 | 0.428 | |
| runGenericTests | 0.336 | 0.009 | 0.344 | |
| testContext | 0.703 | 0.000 | 0.704 | |
| testThat | 0.514 | 0.000 | 0.513 | |
| upgradeExtPkg | 1.690 | 0.004 | 1.694 | |
| warn | 0.002 | 0.000 | 0.002 | |
| warn0 | 0.002 | 0.000 | 0.002 | |