Back to Multiple platform build/check report for BioC 3.7 |
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This page was generated on 2018-10-17 08:35:28 -0400 (Wed, 17 Oct 2018).
Package 1221/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
Repitools 1.26.0 Mark Robinson
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | [ OK ] | |||||||
merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
Package: Repitools |
Version: 1.26.0 |
Command: rm -rf Repitools.buildbin-libdir && mkdir Repitools.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Repitools.buildbin-libdir Repitools_1.26.0.tar.gz |
StartedAt: 2018-10-17 06:53:04 -0400 (Wed, 17 Oct 2018) |
EndedAt: 2018-10-17 06:53:55 -0400 (Wed, 17 Oct 2018) |
EllapsedTime: 51.3 seconds |
RetCode: 0 |
Status: OK |
PackageFile: Repitools_1.26.0.zip |
PackageFileSize: 2.395 MiB |
############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf Repitools.buildbin-libdir && mkdir Repitools.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Repitools.buildbin-libdir Repitools_1.26.0.tar.gz ### ############################################################################## ############################################################################## install for i386 * installing *source* package 'Repitools' ... ** libs C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -D R_NO_REMAP -I. -O3 -Wall -std=gnu99 -mtune=generic -c const.c -o const.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -D R_NO_REMAP -I. -O3 -Wall -std=gnu99 -mtune=generic -c hyp2f1.c -o hyp2f1.o In file included from hyp2f1.c:81:0: ./mconf.h:100:0: warning: "DOMAIN" redefined #define DOMAIN 1 /* argument domain error */ ^ In file included from C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include/Rmath.h:45:0, from hyp2f1.c:80: C:/Rtools/mingw_32/i686-w64-mingw32/include/math.h:29:0: note: this is the location of the previous definition #define DOMAIN _DOMAIN ^ In file included from hyp2f1.c:81:0: ./mconf.h:101:0: warning: "SING" redefined #define SING 2 /* argument singularity */ ^ In file included from C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include/Rmath.h:45:0, from hyp2f1.c:80: C:/Rtools/mingw_32/i686-w64-mingw32/include/math.h:30:0: note: this is the location of the previous definition #define SING _SING ^ In file included from hyp2f1.c:81:0: ./mconf.h:102:0: warning: "OVERFLOW" redefined #define OVERFLOW 3 /* overflow range error */ ^ In file included from C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include/Rmath.h:45:0, from hyp2f1.c:80: C:/Rtools/mingw_32/i686-w64-mingw32/include/math.h:31:0: note: this is the location of the previous definition #define OVERFLOW _OVERFLOW ^ In file included from hyp2f1.c:81:0: ./mconf.h:103:0: warning: "UNDERFLOW" redefined #define UNDERFLOW 4 /* underflow range error */ ^ In file included from C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include/Rmath.h:45:0, from hyp2f1.c:80: C:/Rtools/mingw_32/i686-w64-mingw32/include/math.h:32:0: note: this is the location of the previous definition #define UNDERFLOW _UNDERFLOW ^ In file included from hyp2f1.c:81:0: ./mconf.h:104:0: warning: "TLOSS" redefined #define TLOSS 5 /* total loss of precision */ ^ In file included from C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include/Rmath.h:45:0, from hyp2f1.c:80: C:/Rtools/mingw_32/i686-w64-mingw32/include/math.h:33:0: note: this is the location of the previous definition #define TLOSS _TLOSS ^ In file included from hyp2f1.c:81:0: ./mconf.h:105:0: warning: "PLOSS" redefined #define PLOSS 6 /* partial loss of precision */ ^ In file included from C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include/Rmath.h:45:0, from hyp2f1.c:80: C:/Rtools/mingw_32/i686-w64-mingw32/include/math.h:34:0: note: this is the location of the previous definition #define PLOSS _PLOSS ^ C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -D R_NO_REMAP -I. -O3 -Wall -std=gnu99 -mtune=generic -c mtherr.c -o mtherr.o In file included from mtherr.c:58:0: ./mconf.h:100:0: warning: "DOMAIN" redefined #define DOMAIN 1 /* argument domain error */ ^ In file included from C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include/R.h:58:0, from mtherr.c:56: C:/Rtools/mingw_32/i686-w64-mingw32/include/math.h:29:0: note: this is the location of the previous definition #define DOMAIN _DOMAIN ^ In file included from mtherr.c:58:0: ./mconf.h:101:0: warning: "SING" redefined #define SING 2 /* argument singularity */ ^ In file included from C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include/R.h:58:0, from mtherr.c:56: C:/Rtools/mingw_32/i686-w64-mingw32/include/math.h:30:0: note: this is the location of the previous definition #define SING _SING ^ In file included from mtherr.c:58:0: ./mconf.h:102:0: warning: "OVERFLOW" redefined #define OVERFLOW 3 /* overflow range error */ ^ In file included from C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include/R.h:58:0, from mtherr.c:56: C:/Rtools/mingw_32/i686-w64-mingw32/include/math.h:31:0: note: this is the location of the previous definition #define OVERFLOW _OVERFLOW ^ In file included from mtherr.c:58:0: ./mconf.h:103:0: warning: "UNDERFLOW" redefined #define UNDERFLOW 4 /* underflow range error */ ^ In file included from C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include/R.h:58:0, from mtherr.c:56: C:/Rtools/mingw_32/i686-w64-mingw32/include/math.h:32:0: note: this is the location of the previous definition #define UNDERFLOW _UNDERFLOW ^ In file included from mtherr.c:58:0: ./mconf.h:104:0: warning: "TLOSS" redefined #define TLOSS 5 /* total loss of precision */ ^ In file included from C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include/R.h:58:0, from mtherr.c:56: C:/Rtools/mingw_32/i686-w64-mingw32/include/math.h:33:0: note: this is the location of the previous definition #define TLOSS _TLOSS ^ In file included from mtherr.c:58:0: ./mconf.h:105:0: warning: "PLOSS" redefined #define PLOSS 6 /* partial loss of precision */ ^ In file included from C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include/R.h:58:0, from mtherr.c:56: C:/Rtools/mingw_32/i686-w64-mingw32/include/math.h:34:0: note: this is the location of the previous definition #define PLOSS _PLOSS ^ C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o Repitools.dll tmp.def const.o hyp2f1.o mtherr.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/i386 -lR installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/Repitools.buildbin-libdir/Repitools/libs/i386 ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'Repitools' finding HTML links ... done AdjustedCopyEstimate-class html finding level-2 HTML links ... done AffymetrixCdfFile-class html AffymetrixCelSet-class html BAM2GRanges html Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpKkJGN2/R.INSTALL290c46984ed2/Repitools/man/BAM2GRanges.Rd:27: file link 'ScanBamParam' in package 'Rsamtools' does not exist and so has been treated as a topic BayMethList-class html ChromaBlocks html ChromaResults-class html ClusteredScoresList-class html CopyEstimate-class html FastQC-class html GCAdjustParams-class html GCadjustCopy html GCbiasPlots html MappabilitySource-class html QdnaData html ScoresList-class html abcdDNA html absoluteCN html annoDF2GR html annoGR2DF html annotationBlocksCounts html annotationBlocksLookup html annotationCounts html annotationLookup html binPlots html blocksStats html checkProbes html chr21genes html chromosomeCNplots html clusterPlots html cpgBoxPlots html cpgDensityCalc html cpgDensityPlot html determineOffset html empBayes html enrichmentCalc html enrichmentPlot html expr html featureBlocks html featureScores html findClusters html gcContentCalc html genQC html genomeBlocks html getProbePositionsDf html getSampleOffsets html hcRegions html hyper html loadPairFile html loadSampleDirectory html makeWindowLookupTable html mappabilityCalc html maskOut html mergeReplicates html methylEst html multiHeatmap html plotClusters html plotQdnaByCN html processNDF html profilePlots html regionStats html relativeCN html samplesList html sequenceCalc html setCNVOffsets html summarizeScores html writeWig html ** building package indices ** installing vignettes ** testing if installed package can be loaded In R CMD INSTALL install for x64 * installing *source* package 'Repitools' ... ** libs C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -D R_NO_REMAP -I. -O2 -Wall -std=gnu99 -mtune=generic -c const.c -o const.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -D R_NO_REMAP -I. -O2 -Wall -std=gnu99 -mtune=generic -c hyp2f1.c -o hyp2f1.o In file included from hyp2f1.c:81:0: ./mconf.h:100:0: warning: "DOMAIN" redefined #define DOMAIN 1 /* argument domain error */ ^ In file included from C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include/Rmath.h:45:0, from hyp2f1.c:80: C:/Rtools/mingw_64/x86_64-w64-mingw32/include/math.h:29:0: note: this is the location of the previous definition #define DOMAIN _DOMAIN ^ In file included from hyp2f1.c:81:0: ./mconf.h:101:0: warning: "SING" redefined #define SING 2 /* argument singularity */ ^ In file included from C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include/Rmath.h:45:0, from hyp2f1.c:80: C:/Rtools/mingw_64/x86_64-w64-mingw32/include/math.h:30:0: note: this is the location of the previous definition #define SING _SING ^ In file included from hyp2f1.c:81:0: ./mconf.h:102:0: warning: "OVERFLOW" redefined #define OVERFLOW 3 /* overflow range error */ ^ In file included from C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include/Rmath.h:45:0, from hyp2f1.c:80: C:/Rtools/mingw_64/x86_64-w64-mingw32/include/math.h:31:0: note: this is the location of the previous definition #define OVERFLOW _OVERFLOW ^ In file included from hyp2f1.c:81:0: ./mconf.h:103:0: warning: "UNDERFLOW" redefined #define UNDERFLOW 4 /* underflow range error */ ^ In file included from C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include/Rmath.h:45:0, from hyp2f1.c:80: C:/Rtools/mingw_64/x86_64-w64-mingw32/include/math.h:32:0: note: this is the location of the previous definition #define UNDERFLOW _UNDERFLOW ^ In file included from hyp2f1.c:81:0: ./mconf.h:104:0: warning: "TLOSS" redefined #define TLOSS 5 /* total loss of precision */ ^ In file included from C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include/Rmath.h:45:0, from hyp2f1.c:80: C:/Rtools/mingw_64/x86_64-w64-mingw32/include/math.h:33:0: note: this is the location of the previous definition #define TLOSS _TLOSS ^ In file included from hyp2f1.c:81:0: ./mconf.h:105:0: warning: "PLOSS" redefined #define PLOSS 6 /* partial loss of precision */ ^ In file included from C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include/Rmath.h:45:0, from hyp2f1.c:80: C:/Rtools/mingw_64/x86_64-w64-mingw32/include/math.h:34:0: note: this is the location of the previous definition #define PLOSS _PLOSS ^ C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -D R_NO_REMAP -I. -O2 -Wall -std=gnu99 -mtune=generic -c mtherr.c -o mtherr.o In file included from mtherr.c:58:0: ./mconf.h:100:0: warning: "DOMAIN" redefined #define DOMAIN 1 /* argument domain error */ ^ In file included from C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include/R.h:58:0, from mtherr.c:56: C:/Rtools/mingw_64/x86_64-w64-mingw32/include/math.h:29:0: note: this is the location of the previous definition #define DOMAIN _DOMAIN ^ In file included from mtherr.c:58:0: ./mconf.h:101:0: warning: "SING" redefined #define SING 2 /* argument singularity */ ^ In file included from C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include/R.h:58:0, from mtherr.c:56: C:/Rtools/mingw_64/x86_64-w64-mingw32/include/math.h:30:0: note: this is the location of the previous definition #define SING _SING ^ In file included from mtherr.c:58:0: ./mconf.h:102:0: warning: "OVERFLOW" redefined #define OVERFLOW 3 /* overflow range error */ ^ In file included from C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include/R.h:58:0, from mtherr.c:56: C:/Rtools/mingw_64/x86_64-w64-mingw32/include/math.h:31:0: note: this is the location of the previous definition #define OVERFLOW _OVERFLOW ^ In file included from mtherr.c:58:0: ./mconf.h:103:0: warning: "UNDERFLOW" redefined #define UNDERFLOW 4 /* underflow range error */ ^ In file included from C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include/R.h:58:0, from mtherr.c:56: C:/Rtools/mingw_64/x86_64-w64-mingw32/include/math.h:32:0: note: this is the location of the previous definition #define UNDERFLOW _UNDERFLOW ^ In file included from mtherr.c:58:0: ./mconf.h:104:0: warning: "TLOSS" redefined #define TLOSS 5 /* total loss of precision */ ^ In file included from C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include/R.h:58:0, from mtherr.c:56: C:/Rtools/mingw_64/x86_64-w64-mingw32/include/math.h:33:0: note: this is the location of the previous definition #define TLOSS _TLOSS ^ In file included from mtherr.c:58:0: ./mconf.h:105:0: warning: "PLOSS" redefined #define PLOSS 6 /* partial loss of precision */ ^ In file included from C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include/R.h:58:0, from mtherr.c:56: C:/Rtools/mingw_64/x86_64-w64-mingw32/include/math.h:34:0: note: this is the location of the previous definition #define PLOSS _PLOSS ^ C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o Repitools.dll tmp.def const.o hyp2f1.o mtherr.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/Repitools.buildbin-libdir/Repitools/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'Repitools' as Repitools_1.26.0.zip * DONE (Repitools) In R CMD INSTALL In R CMD INSTALL