############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf ShortRead.buildbin-libdir && mkdir ShortRead.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ShortRead.buildbin-libdir ShortRead_1.50.0.tar.gz ### ############################################################################## ############################################################################## install for i386 * installing *source* package 'ShortRead' ... ** using staged installation ********************************************** WARNING: this package has a configure script It probably needs manual configuration ********************************************** ** libs "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Biostrings_stubs.c -o Biostrings_stubs.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c IRanges_stubs.c -o IRanges_stubs.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_init_ShortRead.c -o R_init_ShortRead.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c S4Vectors_stubs.c -o S4Vectors_stubs.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c XVector_stubs.c -o XVector_stubs.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c alphabet.c -o alphabet.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c count.c -o count.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c io.c -o io.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c io_bowtie.c -o io_bowtie.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c io_soap.c -o io_soap.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c readBfaToc.cc -o readBfaToc.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include' -I"c:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c read_maq_map.cc -o read_maq_map.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sampler.c -o sampler.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c trim.c -o trim.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c util.c -o util.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c xsnap.c -o xsnap.o C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o ShortRead.dll tmp.def Biostrings_stubs.o IRanges_stubs.o R_init_ShortRead.o S4Vectors_stubs.o XVector_stubs.o alphabet.o count.o io.o io_bowtie.o io_soap.o readBfaToc.o read_maq_map.o sampler.o trim.o util.o xsnap.o -LC:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -Lc:/extsoft/lib/i386 -Lc:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lR installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/ShortRead.buildbin-libdir/00LOCK-ShortRead/00new/ShortRead/libs/i386 ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'ShortRead' finding HTML links ... done AlignedDataFrame-class html AlignedDataFrame html AlignedRead-class html AlignedRead html BowtieQA-class html ExperimentPath-class html FastqQA-class html Intensity-class html MAQMapQA-class html QA-class html QualityScore-class html QualityScore html RochePath-class html RocheSet-class html RtaIntensity-class html RtaIntensity html SRFilter-class html SRFilterResult-class html SRSet-class html finding level-2 HTML links ... done SRUtil-class html REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/ShortRead.buildbin-libdir/00LOCK-ShortRead/00new/ShortRead/help/srlist.html Sampler-class html ShortRead-class html ShortRead-deprecated html ShortRead-package html ShortReadQ-class html Snapshot-class html SnapshotFunction-class html SolexaExportQA-class html SolexaIntensity-class html SolexaIntensity html SolexaPath-class html SolexaSet-class html SpTrellis-class html accessors html REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/ShortRead.buildbin-libdir/00LOCK-ShortRead/00new/ShortRead/help/experimentPath.html REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/ShortRead.buildbin-libdir/00LOCK-ShortRead/00new/ShortRead/help/solexaPath.html alphabetByCycle html alphabetScore html clean html countLines html deprecated html dotQA-class html dustyScore html filterFastq html polyn html qa html qa2 html REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/ShortRead.buildbin-libdir/00LOCK-ShortRead/00new/ShortRead/help/QA.html readAligned html readBaseQuality html readBfaToc html readFasta html readFastq html readIntensities html readPrb html readQseq html readXStringColumns html renew html report html spViewPerFeature html srFilter html srdistance html srduplicated html tables html trimTails 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 'ShortRead' ... ********************************************** WARNING: this package has a configure script It probably needs manual configuration ********************************************** ** libs "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Biostrings_stubs.c -o Biostrings_stubs.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c IRanges_stubs.c -o IRanges_stubs.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_init_ShortRead.c -o R_init_ShortRead.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c S4Vectors_stubs.c -o S4Vectors_stubs.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c XVector_stubs.c -o XVector_stubs.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c alphabet.c -o alphabet.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c count.c -o count.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c io.c -o io.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c io_bowtie.c -o io_bowtie.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c io_soap.c -o io_soap.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c readBfaToc.cc -o readBfaToc.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c read_maq_map.cc -o read_maq_map.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sampler.c -o sampler.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c trim.c -o trim.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c util.c -o util.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/S4Vectors/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/IRanges/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/XVector/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Biostrings/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c xsnap.c -o xsnap.o C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o ShortRead.dll tmp.def Biostrings_stubs.o IRanges_stubs.o R_init_ShortRead.o S4Vectors_stubs.o XVector_stubs.o alphabet.o count.o io.o io_bowtie.o io_soap.o readBfaToc.o read_maq_map.o sampler.o trim.o util.o xsnap.o -LC:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/ShortRead.buildbin-libdir/ShortRead/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'ShortRead' as ShortRead_1.50.0.zip * DONE (ShortRead)