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BioC 3.3: BUILD BIN report for QuasR on moscato2

This page was generated on 2016-10-13 12:51:10 -0700 (Thu, 13 Oct 2016).

Package 915/1210HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
QuasR 1.12.0
Michael Stadler
Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/QuasR
Last Changed Rev: 117079 / Revision: 122332
Last Changed Date: 2016-05-03 14:20:18 -0700 (Tue, 03 May 2016)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: QuasR
Version: 1.12.0
Command: rm -rf QuasR.buildbin-libdir && mkdir QuasR.buildbin-libdir && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe --arch x64 CMD INSTALL --build --no-multiarch --library=QuasR.buildbin-libdir QuasR_1.12.0.tar.gz
StartedAt: 2016-10-13 11:16:43 -0700 (Thu, 13 Oct 2016)
EndedAt: 2016-10-13 11:19:14 -0700 (Thu, 13 Oct 2016)
EllapsedTime: 151.4 seconds
RetCode: 0
Status:  OK  
PackageFile: QuasR_1.12.0.zip
PackageFileSize: 1.819 MiB

Command output

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###
### Running command:
###
###   rm -rf QuasR.buildbin-libdir && mkdir QuasR.buildbin-libdir && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe --arch x64 CMD INSTALL --build --no-multiarch --library=QuasR.buildbin-libdir QuasR_1.12.0.tar.gz
###
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* installing *source* package 'QuasR' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"E:/biocbld/bbs-3.3-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include"   -I"E:/biocbld/bbs-3.3-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"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"E:/biocbld/bbs-3.3-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include"   -I"E:/biocbld/bbs-3.3-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"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"E:/biocbld/bbs-3.3-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include"   -I"E:/biocbld/bbs-3.3-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"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"E:/biocbld/bbs-3.3-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include"   -I"E:/biocbld/bbs-3.3-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"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"E:/biocbld/bbs-3.3-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include"   -I"E:/biocbld/bbs-3.3-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"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"E:/biocbld/bbs-3.3-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include"   -I"E:/biocbld/bbs-3.3-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"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"E:/biocbld/bbs-3.3-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include"   -I"E:/biocbld/bbs-3.3-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"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"E:/biocbld/bbs-3.3-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include"   -I"E:/biocbld/bbs-3.3-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"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"E:/biocbld/bbs-3.3-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include"   -I"E:/biocbld/bbs-3.3-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"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"E:/biocbld/bbs-3.3-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include"   -I"E:/biocbld/bbs-3.3-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"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"E:/biocbld/bbs-3.3-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include"   -I"E:/biocbld/bbs-3.3-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"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"E:/biocbld/bbs-3.3-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include"   -I"E:/biocbld/bbs-3.3-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"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"E:/biocbld/bbs-3.3-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include"   -I"E:/biocbld/bbs-3.3-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"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"E:/biocbld/bbs-3.3-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include"   -I"E:/biocbld/bbs-3.3-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"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"E:/biocbld/bbs-3.3-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include"   -I"E:/biocbld/bbs-3.3-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"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"E:/biocbld/bbs-3.3-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include"   -I"E:/biocbld/bbs-3.3-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 E:/biocbld/bbs-3.3-bioc/R/library/Rsamtools/usrlib/x64/libbam.a E:/biocbld/bbs-3.3-bioc/R/library/Rsamtools/usrlib/x64/libbam.a E:/biocbld/bbs-3.3-bioc/R/library/Rsamtools/usrlib/x64/libbcf.a E:/biocbld/bbs-3.3-bioc/R/library/Rsamtools/usrlib/x64/libtabix.a -lws2_32 -pthread -LE:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -Lc:/local323/lib/x64 -Lc:/local323/lib -LE:/biocbld/bbs-3.3-bioc/R/bin/x64 -lR
installing to E:/biocbld/bbs-3.3-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_1.12.0.zip
* DONE (QuasR)