Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2021-10-23 14:06:53 -0400 (Sat, 23 Oct 2021).

CHECK results for biodb on merida1

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 175/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biodb 1.1.16  (landing page)
Pierrick Roger
Snapshot Date: 2021-10-22 14:50:11 -0400 (Fri, 22 Oct 2021)
git_url: https://git.bioconductor.org/packages/biodb
git_branch: master
git_last_commit: c231763
git_last_commit_date: 2021-10-19 06:21:44 -0400 (Tue, 19 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: biodb
Version: 1.1.16
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biodb.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biodb_1.1.16.tar.gz
StartedAt: 2021-10-23 01:16:04 -0400 (Sat, 23 Oct 2021)
EndedAt: 2021-10-23 01:21:56 -0400 (Sat, 23 Oct 2021)
EllapsedTime: 351.9 seconds
RetCode: 0
Status:   OK  
CheckDir: biodb.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biodb.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biodb_1.1.16.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/biodb.Rcheck’
* using R version 4.1.1 Patched (2021-08-22 r80813)
* 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 ‘1.1.16’
* 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 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-3.14-bioc/meat/biodb.Rcheck/00check.log’
for details.



Installation output

biodb.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/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 Patched (2021-08-22 r80813) -- "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 0 | SKIP 0 | PASS 1493 ]
> 
> proc.time()
   user  system elapsed 
179.085  10.513 214.478 

Example timings

biodb.Rcheck/biodb-Ex.timings

nameusersystemelapsed
BiodbConfig2.5390.5253.072
BiodbConn0.6180.0220.643
BiodbConnBase0.4140.0140.430
BiodbCsvEntry0.0160.0010.018
BiodbDbInfo0.4000.0160.419
BiodbDbsInfo0.4290.0210.451
BiodbEntry0.8580.0230.887
BiodbEntryField0.4270.0160.444
BiodbEntryFields0.3930.0180.413
BiodbFactory0.5810.0240.612
BiodbHtmlEntry000
BiodbJsonEntry0.0000.0010.001
BiodbListEntry0.0010.0000.000
BiodbMain0.4030.0220.429
BiodbPersistentCache1.5900.0261.624
BiodbRequest0.7670.0361.649
BiodbRequestScheduler0.5070.0221.615
BiodbSdfEntry0.0000.0000.001
BiodbTestMsgAck0.2140.0150.234
BiodbTxtEntry000
BiodbUrl0.0010.0000.001
BiodbXmlEntry0.0000.0010.000
CompCsvFileConn0.4190.0200.443
CompCsvFileEntry0.5010.0230.527
CompSqliteConn0.4600.0210.484
CompSqliteEntry0.4830.0180.505
CsvFileConn0.5750.0190.596
ExtConnClass0.2660.0070.276
ExtCpp0.4410.0090.455
ExtDefinitions0.1110.0020.114
ExtDescriptionFile0.1140.0030.117
ExtEntryClass0.1030.0030.107
ExtFileGenerator0.1060.0020.109
ExtGenerator2.1760.0512.261
ExtGitignore0.1020.0040.106
ExtLicense0.1400.0040.145
ExtMakefile0.2140.0050.221
ExtPackage2.6890.0402.743
ExtPackageFile0.0620.0010.063
ExtRbuildignore0.0940.0020.096
ExtReadme0.0840.0020.087
ExtTests0.9900.0151.010
ExtTravisFile0.0780.0020.082
ExtVignette0.2320.0030.239
MassCsvFileConn0.6640.0440.716
MassCsvFileEntry0.5880.0220.614
MassSqliteConn0.3460.0160.363
MassSqliteEntry0.3960.0200.420
Progress0.0060.0010.007
Range0.0690.0010.071
SqliteConn0.4030.0230.430
TestRefEntries0.0200.0010.021
checkDeprecatedCacheFolders0.0010.0000.001
createBiodbTestInstance0.1770.0120.192
df2str0.0020.0000.002
error0.0030.0000.003
error00.0020.0000.003
genNewExtPkg1.8670.0241.923
getConnClassName000
getConnTypes000
getDefaultCacheDir000
getEntryClassName0.0000.0010.000
getEntryTypes000
getLicenses000
getLogger0.0050.0010.004
getPkgName000
getReposName000
getTestOutputDir000
listTestRefEntries0.0160.0000.016
logDebug000
logDebug00.0010.0000.000
logInfo0.0020.0000.002
logInfo00.0020.0010.001
logTrace0.0010.0000.001
logTrace00.0000.0000.001
lst2str0.0000.0000.001
newInst0.3000.0150.318
runGenericTests0.1320.0100.143
testContext0.5830.0160.600
testThat0.2410.0130.256
upgradeExtPkg2.1440.0342.193
warn0.0020.0000.002
warn00.0030.0000.003