BioC 3.5: BUILD BIN report for QuasR on tokay2

Package: QuasR

Version: 1.16.0

Command: rm -rf QuasR.buildbin-libdir && mkdir QuasR.buildbin-libdir && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe --arch x64 CMD INSTALL --build --no-multiarch --library=QuasR.buildbin-libdir QuasR_1.16.0.tar.gz

StartedAt: 2017-10-18 04:54:05 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 04:56:18 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 133.0 seconds

RetCode: 0

Status:  OK

PackageFile: QuasR_1.16.0.zip

PackageFileSize: 1.874 MiB

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### Running command:
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###   rm -rf QuasR.buildbin-libdir && mkdir QuasR.buildbin-libdir && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe --arch x64 CMD INSTALL --build --no-multiarch --library=QuasR.buildbin-libdir QuasR_1.16.0.tar.gz
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* installing *source* package 'QuasR' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c R_init_QuasR.cpp -o R_init_QuasR.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include"   -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c cat_bam.c -o cat_bam.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include"   -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c convert_reads_id_bis_rc.c -o convert_reads_id_bis_rc.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include"   -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c count_alignments.c -o count_alignments.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include"   -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c count_alignments_subregions.c -o count_alignments_subregions.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c count_junctions.cpp -o count_junctions.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include"   -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c export_wig.c -o export_wig.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include"   -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c extract_unmapped_reads.c -o extract_unmapped_reads.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include"   -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c idxstats_bam.c -o idxstats_bam.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c merge_reorder_sam.cpp -o merge_reorder_sam.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include"   -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c nucleotide_alignment_frequencies.c -o nucleotide_alignment_frequencies.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include"   -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c profile_alignments.c -o profile_alignments.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=core2 -c quantify_methylation.cpp -o quantify_methylation.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include"   -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c remove_unmapped_from_sam.c -o remove_unmapped_from_sam.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include"   -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c split_sam_chr.c -o split_sam_chr.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include"   -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c utilities.c -o utilities.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o QuasR.dll tmp.def R_init_QuasR.o cat_bam.o convert_reads_id_bis_rc.o count_alignments.o count_alignments_subregions.o count_junctions.o export_wig.o extract_unmapped_reads.o idxstats_bam.o merge_reorder_sam.o nucleotide_alignment_frequencies.o profile_alignments.o quantify_methylation.o remove_unmapped_from_sam.o split_sam_chr.o utilities.o C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/usrlib/x64/libbam.a C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/usrlib/x64/libbam.a C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/usrlib/x64/libbcf.a C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/usrlib/x64/libtabix.a -lws2_32 -pthread -LC:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/biocbuild/bbs-3.5-bioc/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/QuasR.buildbin-libdir/QuasR/libs/x64
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'QuasR' as QuasR_1.16.0.zip
* DONE (QuasR)