Package: motifcounter

Version: 1.7.0

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:motifcounter.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings motifcounter_1.7.0.tar.gz

StartedAt: 2019-04-09 04:23:06 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 04:52:25 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 1759.2 seconds

RetCode: 0

Status:  OK

CheckDir: motifcounter.Rcheck

Warnings: 0

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:motifcounter.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings motifcounter_1.7.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/motifcounter.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* 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 '1.7.0'
* 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 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-3.9-bioc/R/library/motifcounter/libs/i386/motifcounter.dll':
  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-3.9-bioc/R/library/motifcounter/libs/x64/motifcounter.dll':
  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 or elapsed time > 5s
                       user system elapsed
simulateClumpSizeDist 11.20   0.50   11.70
motifEnrichment        4.31   0.72    5.03
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
simulateClumpSizeDist 12.47   0.56   13.04
* 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-3.9-bioc/meat/motifcounter.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/motifcounter_1.7.0.tar.gz && rm -rf motifcounter.buildbin-libdir && mkdir motifcounter.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=motifcounter.buildbin-libdir motifcounter_1.7.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL motifcounter_1.7.0.zip && rm motifcounter_1.7.0.tar.gz motifcounter_1.7.0.zip
###
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100  383k  100  383k    0     0  3731k      0 --:--:-- --:--:-- --:--:-- 3998k

install for i386

* installing *source* package 'motifcounter' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O3 -Wall  -std=gnu99 -mtune=generic -c Rbackground.c -o Rbackground.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O3 -Wall  -std=gnu99 -mtune=generic -c Rcombinatorial.c -o Rcombinatorial.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O3 -Wall  -std=gnu99 -mtune=generic -c Rcompoundpoisson.c -o Rcompoundpoisson.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O3 -Wall  -std=gnu99 -mtune=generic -c Rminmaxscore.c -o Rminmaxscore.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O3 -Wall  -std=gnu99 -mtune=generic -c Roption.c -o Roption.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O3 -Wall  -std=gnu99 -mtune=generic -c Roverlap.c -o Roverlap.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O3 -Wall  -std=gnu99 -mtune=generic -c Rscore1d.c -o Rscore1d.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O3 -Wall  -std=gnu99 -mtune=generic -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:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O3 -Wall  -std=gnu99 -mtune=generic -c Rsimulate.c -o Rsimulate.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O3 -Wall  -std=gnu99 -mtune=generic -c background.c -o background.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O3 -Wall  -std=gnu99 -mtune=generic -c combinatorial.c -o combinatorial.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O3 -Wall  -std=gnu99 -mtune=generic -c compoundpoisson.c -o compoundpoisson.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O3 -Wall  -std=gnu99 -mtune=generic -c markovchain.c -o markovchain.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O3 -Wall  -std=gnu99 -mtune=generic -c markovchain_single.c -o markovchain_single.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O3 -Wall  -std=gnu99 -mtune=generic -c matrix.c -o matrix.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O3 -Wall  -std=gnu99 -mtune=generic -c mdist_register.c -o mdist_register.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O3 -Wall  -std=gnu99 -mtune=generic -c minmaxscore.c -o minmaxscore.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O3 -Wall  -std=gnu99 -mtune=generic -c overlap.c -o overlap.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O3 -Wall  -std=gnu99 -mtune=generic -c score1d.c -o score1d.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O3 -Wall  -std=gnu99 -mtune=generic -c score2d.c -o score2d.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O3 -Wall  -std=gnu99 -mtune=generic -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:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O3 -Wall  -std=gnu99 -mtune=generic -c sequence.c -o sequence.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O3 -Wall  -std=gnu99 -mtune=generic -c simulate.c -o simulate.o
C:/Rtools/mingw_32/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˜1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-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:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mtune=generic -c Rbackground.c -o Rbackground.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mtune=generic -c Rcombinatorial.c -o Rcombinatorial.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mtune=generic -c Rcompoundpoisson.c -o Rcompoundpoisson.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mtune=generic -c Rminmaxscore.c -o Rminmaxscore.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mtune=generic -c Roption.c -o Roption.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mtune=generic -c Roverlap.c -o Roverlap.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mtune=generic -c Rscore1d.c -o Rscore1d.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mtune=generic -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:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mtune=generic -c Rsimulate.c -o Rsimulate.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mtune=generic -c background.c -o background.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mtune=generic -c combinatorial.c -o combinatorial.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mtune=generic -c compoundpoisson.c -o compoundpoisson.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mtune=generic -c markovchain.c -o markovchain.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mtune=generic -c markovchain_single.c -o markovchain_single.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mtune=generic -c matrix.c -o matrix.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mtune=generic -c mdist_register.c -o mdist_register.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mtune=generic -c minmaxscore.c -o minmaxscore.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mtune=generic -c overlap.c -o overlap.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mtune=generic -c score1d.c -o score1d.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mtune=generic -c score2d.c -o score2d.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mtune=generic -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:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mtune=generic -c sequence.c -o sequence.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"  -fopenmp -DIN_R   -O2 -Wall  -std=gnu99 -mtune=generic -c simulate.c -o simulate.o
C:/Rtools/mingw_64/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˜1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/motifcounter.buildbin-libdir/motifcounter/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'motifcounter' as motifcounter_1.7.0.zip
* DONE (motifcounter)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'motifcounter' successfully unpacked and MD5 sums checked

R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
Copyright (C) 2019 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")
== testthat results  ===========================================================
OK: 841 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 534.29  361.32  896.43 

R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
Copyright (C) 2019 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")
== testthat results  ===========================================================
OK: 841 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 348.10  332.54  695.96