Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:06:56 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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

CHECK results for motifcounter on tokay2


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? 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: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
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 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 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: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:motifcounter.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings motifcounter_1.18.0.tar.gz
StartedAt: 2022-04-12 23:11:36 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 23:23:46 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 730.2 seconds
RetCode: 0
Status:   OK  
CheckDir: motifcounter.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:motifcounter.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings motifcounter_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/motifcounter.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/motifcounter/libs/i386/motifcounter.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/motifcounter/libs/x64/motifcounter.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
simulateClumpSizeDist 8.76   0.26    9.03
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
simulateClumpSizeDist  9.1   0.44    9.53
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/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:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/motifcounter_1.18.0.tar.gz && rm -rf motifcounter.buildbin-libdir && mkdir motifcounter.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=motifcounter.buildbin-libdir motifcounter_1.18.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL motifcounter_1.18.0.zip && rm motifcounter_1.18.0.tar.gz motifcounter_1.18.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 94  387k   94  366k    0     0   654k      0 --:--:-- --:--:-- --:--:--  654k
100  387k  100  387k    0     0   689k      0 --:--:-- --:--:-- --:--:--  690k

install for i386

* installing *source* package 'motifcounter' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c Rbackground.c -o Rbackground.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c Rcombinatorial.c -o Rcombinatorial.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c Rcompoundpoisson.c -o Rcompoundpoisson.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c Rminmaxscore.c -o Rminmaxscore.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c Roption.c -o Roption.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c Roverlap.c -o Roverlap.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c Rscore1d.c -o Rscore1d.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c Rsequence.c -o Rsequence.o
Rsequence.c: In function 'RscoreHistogram':
Rsequence.c:143:21: warning: unused variable 'noscores' [-Wunused-variable]
     int mins, maxs, noscores;
                     ^~~~~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c Rsimulate.c -o Rsimulate.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c background.c -o background.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c combinatorial.c -o combinatorial.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c compoundpoisson.c -o compoundpoisson.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c markovchain.c -o markovchain.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c markovchain_single.c -o markovchain_single.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c matrix.c -o matrix.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c mdist_register.c -o mdist_register.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c minmaxscore.c -o minmaxscore.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c overlap.c -o overlap.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c score1d.c -o score1d.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c score2d.c -o score2d.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c scorefunctions.c -o scorefunctions.o
scorefunctions.c: In function 'getPositionWeights':
scorefunctions.c:84:22: warning: unused variable 'cindex' [-Wunused-variable]
     int j, i, index, cindex, ds;
                      ^~~~~~
scorefunctions.c: In function 'hitSequence':
scorefunctions.c:119:17: warning: unused variable 'cindex' [-Wunused-variable]
   int s, index, cindex;
                 ^~~~~~
scorefunctions.c: In function 'scoreSequence':
scorefunctions.c:159:19: warning: unused variable 'cindex' [-Wunused-variable]
     int s, index, cindex;
                   ^~~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c sequence.c -o sequence.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c simulate.c -o simulate.o
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o motifcounter.dll tmp.def 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 -fopenmp -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/motifcounter.buildbin-libdir/00LOCK-motifcounter/00new/motifcounter/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'motifcounter'
    finding HTML links ... done
    Background-class                        html  
    Overlap-class                           html  
    clumpSizeDist                           html  
    combinatorialDist                       html  
    compoundPoissonDist                     html  
    computeClumpStartProb                   html  
    generateDNAString                       html  
    generateDNAStringSet                    html  
    getAlpha                                html  
    getBeta                                 html  
    getBeta3p                               html  
    getBeta5p                               html  
    getCounts                               html  
    getGamma                                html  
    getOrder                                html  
    getSinglestranded                       html  
    getStation                              html  
    getTrans                                html  
    hitStrand                               html  
    lenSequences                            html  
    markovModel                             html  
    motifAndBackgroundValid                 html  
    motifEnrichment                         html  
    motifHitProfile                         html  
    motifHits                               html  
    motifValid                              html  
    motifcounter-package                    html  
    motifcounterOptions                     html  
    normalizeMotif                          html  
    numMotifHits                            html  
    probOverlapHit                          html  
    readBackground                          html  
    revcompMotif                            html  
    scoreDist                               html  
    scoreDistBf                             html  
    scoreDistEmpirical                      html  
    scoreHistogram                          html  
    scoreHistogramSingleSeq                 html  
    scoreProfile                            html  
    scoreSequence                           html  
    scoreStrand                             html  
    scoreThreshold                          html  
    sigLevel                                html  
    simulateClumpSizeDist                   html  
    simulateNumHitsDist                     html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'motifcounter' ...
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c Rbackground.c -o Rbackground.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c Rcombinatorial.c -o Rcombinatorial.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c Rcompoundpoisson.c -o Rcompoundpoisson.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c Rminmaxscore.c -o Rminmaxscore.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c Roption.c -o Roption.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c Roverlap.c -o Roverlap.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c Rscore1d.c -o Rscore1d.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c Rsequence.c -o Rsequence.o
Rsequence.c: In function 'RscoreHistogram':
Rsequence.c:143:21: warning: unused variable 'noscores' [-Wunused-variable]
     int mins, maxs, noscores;
                     ^~~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c Rsimulate.c -o Rsimulate.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c background.c -o background.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c combinatorial.c -o combinatorial.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c compoundpoisson.c -o compoundpoisson.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c markovchain.c -o markovchain.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c markovchain_single.c -o markovchain_single.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c matrix.c -o matrix.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c mdist_register.c -o mdist_register.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c minmaxscore.c -o minmaxscore.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c overlap.c -o overlap.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c score1d.c -o score1d.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c score2d.c -o score2d.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c scorefunctions.c -o scorefunctions.o
scorefunctions.c: In function 'getPositionWeights':
scorefunctions.c:84:22: warning: unused variable 'cindex' [-Wunused-variable]
     int j, i, index, cindex, ds;
                      ^~~~~~
scorefunctions.c: In function 'hitSequence':
scorefunctions.c:119:17: warning: unused variable 'cindex' [-Wunused-variable]
   int s, index, cindex;
                 ^~~~~~
scorefunctions.c: In function 'scoreSequence':
scorefunctions.c:159:19: warning: unused variable 'cindex' [-Wunused-variable]
     int s, index, cindex;
                   ^~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c sequence.c -o sequence.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c simulate.c -o simulate.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o motifcounter.dll tmp.def 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 -fopenmp -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/motifcounter.buildbin-libdir/motifcounter/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'motifcounter' as motifcounter_1.18.0.zip
* DONE (motifcounter)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'motifcounter' successfully unpacked and MD5 sums checked

Tests output

motifcounter.Rcheck/tests_i386/testthat.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 841 ]
> 
> proc.time()
   user  system elapsed 
 222.57   64.26  287.01 

motifcounter.Rcheck/tests_x64/testthat.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 841 ]
> 
> proc.time()
   user  system elapsed 
 210.73   72.78  284.35 

Example timings

motifcounter.Rcheck/examples_i386/motifcounter-Ex.timings

nameusersystemelapsed
clumpSizeDist0.410.080.53
combinatorialDist0.350.140.50
compoundPoissonDist0.410.110.51
computeClumpStartProb0.220.050.27
generateDNAString0.070.000.07
generateDNAStringSet0.130.000.13
hitStrand0.060.000.06
lenSequences0.060.000.06
markovModel0.160.030.19
motifAndBackgroundValid0.070.000.08
motifEnrichment2.770.112.87
motifHitProfile0.060.000.06
motifHits0.080.000.08
motifValid000
motifcounter-package1.200.131.34
motifcounterOptions000
normalizeMotif000
numMotifHits0.50.00.5
probOverlapHit0.390.060.45
readBackground0.060.000.06
revcompMotif000
scoreDist0.080.000.08
scoreDistBf0.110.000.11
scoreDistEmpirical2.840.002.84
scoreHistogram0.190.000.19
scoreHistogramSingleSeq0.080.000.08
scoreProfile0.370.000.37
scoreSequence0.070.000.07
scoreStrand0.070.000.07
scoreThreshold0.070.000.07
sigLevel000
simulateClumpSizeDist8.760.269.03
simulateNumHitsDist1.990.082.06

motifcounter.Rcheck/examples_x64/motifcounter-Ex.timings

nameusersystemelapsed
clumpSizeDist0.180.040.20
combinatorialDist0.290.000.30
compoundPoissonDist0.300.060.36
computeClumpStartProb0.160.010.17
generateDNAString0.070.000.08
generateDNAStringSet0.220.000.22
hitStrand0.130.000.12
lenSequences0.110.000.11
markovModel0.190.050.24
motifAndBackgroundValid0.090.000.09
motifEnrichment2.750.052.81
motifHitProfile0.060.010.08
motifHits0.080.000.08
motifValid000
motifcounter-package1.250.141.39
motifcounterOptions000
normalizeMotif000
numMotifHits0.620.000.62
probOverlapHit0.210.070.27
readBackground0.080.000.08
revcompMotif000
scoreDist0.070.000.08
scoreDistBf0.110.000.10
scoreDistEmpirical3.050.033.08
scoreHistogram0.310.000.32
scoreHistogramSingleSeq0.120.000.13
scoreProfile0.600.000.59
scoreSequence0.100.000.09
scoreStrand0.070.000.08
scoreThreshold0.080.010.09
sigLevel000
simulateClumpSizeDist9.100.449.53
simulateNumHitsDist1.650.031.69