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INSTALL report for motifcounter on tokay1

This page was generated on 2019-04-13 11:27:39 -0400 (Sat, 13 Apr 2019).

Package 994/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
motifcounter 1.6.0
Wolfgang Kopp
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/motifcounter
Branch: RELEASE_3_8
Last Commit: a7d2a37
Last Changed Date: 2018-10-30 11:42:04 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64 [ OK ] OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: motifcounter
Version: 1.6.0
Command: C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/motifcounter_1.6.0.tar.gz && rm -rf motifcounter.buildbin-libdir && mkdir motifcounter.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=motifcounter.buildbin-libdir motifcounter_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL motifcounter_1.6.0.zip && rm motifcounter_1.6.0.tar.gz motifcounter_1.6.0.zip
StartedAt: 2019-04-12 19:11:44 -0400 (Fri, 12 Apr 2019)
EndedAt: 2019-04-12 19:12:57 -0400 (Fri, 12 Apr 2019)
EllapsedTime: 73.3 seconds
RetCode: 0
Status:  OK  

Command output

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/motifcounter_1.6.0.tar.gz && rm -rf motifcounter.buildbin-libdir && mkdir motifcounter.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=motifcounter.buildbin-libdir motifcounter_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL motifcounter_1.6.0.zip && rm motifcounter_1.6.0.tar.gz motifcounter_1.6.0.zip
###
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100  382k  100  382k    0     0  9578k      0 --:--:-- --:--:-- --:--:-- 10.3M

install for i386

* installing *source* package 'motifcounter' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-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˜1.8-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˜1.8-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˜1.8-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˜1.8-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˜1.8-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˜1.8-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˜1.8-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˜1.8-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˜1.8-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˜1.8-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˜1.8-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˜1.8-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˜1.8-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˜1.8-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˜1.8-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˜1.8-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˜1.8-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˜1.8-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˜1.8-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˜1.8-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˜1.8-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˜1.8-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˜1.8-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/motifcounter.buildbin-libdir/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
In R CMD INSTALL

install for x64

* installing *source* package 'motifcounter' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-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˜1.8-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˜1.8-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˜1.8-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˜1.8-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˜1.8-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˜1.8-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˜1.8-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˜1.8-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˜1.8-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˜1.8-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˜1.8-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˜1.8-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˜1.8-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˜1.8-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˜1.8-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˜1.8-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˜1.8-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˜1.8-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˜1.8-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˜1.8-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˜1.8-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˜1.8-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˜1.8-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/motifcounter.buildbin-libdir/motifcounter/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'motifcounter' as motifcounter_1.6.0.zip
* DONE (motifcounter)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'motifcounter' successfully unpacked and MD5 sums checked
In R CMD INSTALL