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This page was generated on 2021-12-03 13:05:54 -0500 (Fri, 03 Dec 2021).

CHECK results for motifcounter on machv2

To the developers/maintainers of the motifcounter package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/motifcounter.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 1201/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
motifcounter 1.18.0  (landing page)
Wolfgang Kopp
Snapshot Date: 2021-12-02 01:55:06 -0500 (Thu, 02 Dec 2021)
git_url: https://git.bioconductor.org/packages/motifcounter
git_branch: RELEASE_3_14
git_last_commit: 6628a11
git_last_commit_date: 2021-10-26 12:34:00 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 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: motifcounter
Version: 1.18.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:motifcounter.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings motifcounter_1.18.0.tar.gz
StartedAt: 2021-12-02 16:47:32 -0500 (Thu, 02 Dec 2021)
EndedAt: 2021-12-02 16:52:15 -0500 (Thu, 02 Dec 2021)
EllapsedTime: 282.8 seconds
RetCode: 0
Status:   OK  
CheckDir: motifcounter.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:motifcounter.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings motifcounter_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/motifcounter.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘motifcounter/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘motifcounter’ version ‘1.18.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .zenodo.json
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘motifcounter’ 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 line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
simulateClumpSizeDist 15.919  0.347   16.28
* 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
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/motifcounter.Rcheck/00check.log’
for details.



Installation output

motifcounter.Rcheck/00install.out

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##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL motifcounter
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘motifcounter’ ...
** using staged installation
** libs
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -DIN_R -fPIC  -Wall -g -O2  -c Rbackground.c -o Rbackground.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -DIN_R -fPIC  -Wall -g -O2  -c Rcombinatorial.c -o Rcombinatorial.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -DIN_R -fPIC  -Wall -g -O2  -c Rcompoundpoisson.c -o Rcompoundpoisson.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -DIN_R -fPIC  -Wall -g -O2  -c Rminmaxscore.c -o Rminmaxscore.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -DIN_R -fPIC  -Wall -g -O2  -c Roption.c -o Roption.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -DIN_R -fPIC  -Wall -g -O2  -c Roverlap.c -o Roverlap.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -DIN_R -fPIC  -Wall -g -O2  -c Rscore1d.c -o Rscore1d.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -DIN_R -fPIC  -Wall -g -O2  -c Rsequence.c -o Rsequence.o
Rsequence.c:143:21: warning: unused variable 'noscores' [-Wunused-variable]
    int mins, maxs, noscores;
                    ^
1 warning generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -DIN_R -fPIC  -Wall -g -O2  -c Rsimulate.c -o Rsimulate.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -DIN_R -fPIC  -Wall -g -O2  -c background.c -o background.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -DIN_R -fPIC  -Wall -g -O2  -c combinatorial.c -o combinatorial.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -DIN_R -fPIC  -Wall -g -O2  -c compoundpoisson.c -o compoundpoisson.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -DIN_R -fPIC  -Wall -g -O2  -c markovchain.c -o markovchain.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -DIN_R -fPIC  -Wall -g -O2  -c markovchain_single.c -o markovchain_single.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -DIN_R -fPIC  -Wall -g -O2  -c matrix.c -o matrix.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -DIN_R -fPIC  -Wall -g -O2  -c mdist_register.c -o mdist_register.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -DIN_R -fPIC  -Wall -g -O2  -c minmaxscore.c -o minmaxscore.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -DIN_R -fPIC  -Wall -g -O2  -c overlap.c -o overlap.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -DIN_R -fPIC  -Wall -g -O2  -c score1d.c -o score1d.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -DIN_R -fPIC  -Wall -g -O2  -c score2d.c -o score2d.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -DIN_R -fPIC  -Wall -g -O2  -c scorefunctions.c -o scorefunctions.o
scorefunctions.c:84:22: warning: unused variable 'cindex' [-Wunused-variable]
    int j, i, index, cindex, ds;
                     ^
scorefunctions.c:119:17: warning: unused variable 'cindex' [-Wunused-variable]
  int s, index, cindex;
                ^
scorefunctions.c:159:19: warning: unused variable 'cindex' [-Wunused-variable]
    int s, index, cindex;
                  ^
3 warnings generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -DIN_R -fPIC  -Wall -g -O2  -c sequence.c -o sequence.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -DIN_R -fPIC  -Wall -g -O2  -c simulate.c -o simulate.o
clang -mmacosx-version-min=10.13 -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 motifcounter.so Rbackground.o Rcombinatorial.o Rcompoundpoisson.o Rminmaxscore.o Roption.o Roverlap.o Rscore1d.o Rsequence.o Rsimulate.o background.o combinatorial.o compoundpoisson.o markovchain.o markovchain_single.o matrix.o mdist_register.o minmaxscore.o overlap.o score1d.o score2d.o scorefunctions.o sequence.o simulate.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.1/Resources/library/00LOCK-motifcounter/00new/motifcounter/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 (motifcounter)

Tests output

motifcounter.Rcheck/tests/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
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.

> library(testthat)
> library(motifcounter)
> 
> test_check("motifcounter")
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 841 ]
> 
> proc.time()
   user  system elapsed 
145.572   1.677 147.368 

Example timings

motifcounter.Rcheck/motifcounter-Ex.timings

nameusersystemelapsed
clumpSizeDist0.1900.0200.213
combinatorialDist0.3400.0170.357
compoundPoissonDist0.2420.0080.251
computeClumpStartProb0.1610.0040.165
generateDNAString0.1100.0010.111
generateDNAStringSet0.1940.0110.204
hitStrand0.1440.0180.161
lenSequences0.1360.0170.154
markovModel0.1800.0050.186
motifAndBackgroundValid0.1290.0010.132
motifEnrichment3.5560.0213.579
motifHitProfile0.1090.0030.112
motifHits0.1250.0050.129
motifValid0.0010.0000.002
motifcounter-package1.1140.0241.142
motifcounterOptions000
normalizeMotif0.0020.0010.002
numMotifHits0.7770.0110.792
probOverlapHit0.1990.0020.202
readBackground0.1080.0010.109
revcompMotif0.0020.0010.003
scoreDist0.1230.0010.124
scoreDistBf0.1620.0010.164
scoreDistEmpirical3.5550.0393.598
scoreHistogram0.2970.0120.311
scoreHistogramSingleSeq0.1420.0120.153
scoreProfile0.6150.0040.620
scoreSequence0.0850.0030.087
scoreStrand0.0880.0020.090
scoreThreshold0.0960.0010.098
sigLevel000
simulateClumpSizeDist15.919 0.34716.280
simulateNumHitsDist2.5130.0502.564