Wolfgang Kopp
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/motifcounter |
| Branch: RELEASE_3_11 |
| Last Commit: 0ca6d8a |
| Last Changed Date: 2020-04-27 15:06:23 -0400 (Mon, 27 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:57:11 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE motifcounter PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1125/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| motifcounter 1.12.0 Wolfgang Kopp
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | [ OK ] | OK | OK | OK | | ||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |
| Package: motifcounter |
| Version: 1.12.0 |
| Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/motifcounter_1.12.0.tar.gz && rm -rf motifcounter.buildbin-libdir && mkdir motifcounter.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=motifcounter.buildbin-libdir motifcounter_1.12.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL motifcounter_1.12.0.zip && rm motifcounter_1.12.0.tar.gz motifcounter_1.12.0.zip |
| StartedAt: 2020-10-16 17:23:44 -0400 (Fri, 16 Oct 2020) |
| EndedAt: 2020-10-16 17:25:11 -0400 (Fri, 16 Oct 2020) |
| EllapsedTime: 86.9 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/motifcounter_1.12.0.tar.gz && rm -rf motifcounter.buildbin-libdir && mkdir motifcounter.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=motifcounter.buildbin-libdir motifcounter_1.12.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL motifcounter_1.12.0.zip && rm motifcounter_1.12.0.tar.gz motifcounter_1.12.0.zip
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% Total % Received % Xferd Average Speed Time Time Time Current
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install for i386
* installing *source* package 'motifcounter' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/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-3~1.11-/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-3~1.11-/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-3~1.11-/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-3~1.11-/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-3~1.11-/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-3~1.11-/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-3~1.11-/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-3~1.11-/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-3~1.11-/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-3~1.11-/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-3~1.11-/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-3~1.11-/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-3~1.11-/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-3~1.11-/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-3~1.11-/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-3~1.11-/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-3~1.11-/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-3~1.11-/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-3~1.11-/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-3~1.11-/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-3~1.11-/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-3~1.11-/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-3~1.11-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.11-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-3~1.11-/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-3~1.11-/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-3~1.11-/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-3~1.11-/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-3~1.11-/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-3~1.11-/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-3~1.11-/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-3~1.11-/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-3~1.11-/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-3~1.11-/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-3~1.11-/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-3~1.11-/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-3~1.11-/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-3~1.11-/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-3~1.11-/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-3~1.11-/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-3~1.11-/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-3~1.11-/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-3~1.11-/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-3~1.11-/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-3~1.11-/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-3~1.11-/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-3~1.11-/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-3~1.11-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/motifcounter.buildbin-libdir/motifcounter/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'motifcounter' as motifcounter_1.12.0.zip
* DONE (motifcounter)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'motifcounter' successfully unpacked and MD5 sums checked