Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-10-15 15:06:29 -0400 (Fri, 15 Oct 2021).

CHECK results for biodb on machv2

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.

raw results

Package 178/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biodb 1.0.4  (landing page)
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)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: biodb
Version: 1.0.4
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:biodb.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings biodb_1.0.4.tar.gz
StartedAt: 2021-10-14 16:47:44 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 16:53:32 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 347.7 seconds
RetCode: 0
Status:   OK  
CheckDir: biodb.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:biodb.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings biodb_1.0.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/biodb.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (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 ... OK
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/biodb.Rcheck/00check.log’
for details.



Installation output

biodb.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL biodb
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘biodb’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/testthat/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/testthat/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c closeMatchPpm.cpp -o closeMatchPpm.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/testthat/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c test-100-ms_matching.cpp -o test-100-ms_matching.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/testthat/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c test-runner.cpp -o test-runner.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o biodb.so RcppExports.o closeMatchPpm.o test-100-ms_matching.o test-runner.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.1/Resources/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)

Tests output

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-apple-darwin17.0 (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 
199.568  13.602 221.019 

Example timings

biodb.Rcheck/biodb-Ex.timings

nameusersystemelapsed
BiodbCompounddbConn-class2.9410.5403.501
BiodbConfig-class0.6420.0110.656
BiodbConn-class0.8110.0120.826
BiodbConnBase-class0.6390.0080.650
BiodbCsvEntry-class0.0630.0020.066
BiodbDbInfo-class0.6430.0090.654
BiodbDbsInfo-class0.5860.0090.596
BiodbDownloadable-class0.1440.0010.145
BiodbEditable-class0.7950.0130.899
BiodbEntry-class1.1970.0181.223
BiodbEntryField-class0.6790.0110.693
BiodbEntryFields-class0.5580.0090.569
BiodbFactory-class0.9540.0150.974
BiodbHtmlEntry-class0.0160.0010.017
BiodbJsonEntry-class0.0180.0000.019
BiodbListEntry-class0.0150.0000.016
BiodbMain-class0.5670.0080.578
BiodbMassdbConn-class0.7410.0080.836
BiodbObserver-class0.7910.0110.805
BiodbPersistentCache-class2.5100.0262.544
BiodbRemotedbConn-class1.1720.0271.205
BiodbRequest0.8730.0211.758
BiodbRequestScheduler-class0.7170.0121.378
BiodbSdfEntry-class0.0260.0000.027
BiodbTestMsgAck-class0.5940.0070.603
BiodbTxtEntry-class0.0140.0000.014
BiodbUrl0.0020.0000.002
BiodbWritable-class1.0290.0171.052
BiodbXmlEntry-class0.0260.0000.026
CompCsvFileConn-class0.8340.0080.846
CompCsvFileEntry-class0.8850.0130.902
CompSqliteConn-class0.7660.0140.783
CompSqliteEntry-class0.8050.0110.819
CsvFileConn-class0.9640.0110.978
ExtConnClass0.2620.0050.298
ExtCpp0.4730.0080.481
ExtDefinitions0.1300.0040.134
ExtDescriptionFile0.0970.0030.099
ExtEntryClass0.1410.0020.144
ExtFileGenerator0.1210.0030.124
ExtGenerator2.1380.0332.178
ExtGitignore0.0970.0040.102
ExtLicense0.1410.0040.145
ExtMakefile0.1150.0030.118
ExtPackage2.4680.0392.514
ExtPackageFile0.0880.0020.090
ExtRbuildignore0.0850.0030.087
ExtReadme0.0710.0020.073
ExtTests0.7830.0100.794
ExtTravisFile0.0990.0020.101
ExtVignette0.0850.0030.088
MassCsvFileConn-class1.2190.0171.244
MassCsvFileEntry-class1.1510.0091.165
MassSqliteConn-class0.8070.0100.820
MassSqliteEntry-class0.7580.0090.768
Progress0.0080.0010.009
Range0.0780.0010.079
SqliteConn-class0.7210.0100.771
createBiodbTestInstance0.6280.0070.637
df2str0.0030.0010.004
error0.0010.0000.002
error00.0030.0000.002
genNewExtPkg2.2590.0302.294
getConnClassName0.0000.0000.001
getConnTypes000
getEntryClassName0.0000.0010.000
getEntryTypes000
getLicenses0.0000.0000.001
getLogger0.0050.0000.005
getPkgName0.0000.0010.001
getReposName0.0000.0000.001
getTestOutputDir000
listTestRefEntries0.0000.0010.001
logDebug0.0010.0010.001
logDebug00.0000.0010.001
logInfo0.0020.0000.003
logInfo00.0020.0000.002
logTrace0.0000.0000.001
logTrace00.0010.0000.001
lst2str0.0000.0010.001
newInst0.6050.0070.615
runGenericTests0.5700.0090.578
testContext1.2410.0141.261
testThat0.6920.0100.704
upgradeExtPkg2.3000.0332.982
warn0.0020.0010.003
warn00.0020.0000.003