csaw 1.6.1
Aaron Lun
| 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/csaw | | Last Changed Rev: 117853 / Revision: 122332 | | Last Changed Date: 2016-05-25 11:12:49 -0700 (Wed, 25 May 2016) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | OK | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | [ OK ] | OK | OK | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### rm -rf csaw.buildbin-libdir && mkdir csaw.buildbin-libdir && C:\cygwin\bin\curl.exe -O http://zin2/BBS/3.3/bioc/src/contrib/csaw_1.6.1.tar.gz && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --library=csaw.buildbin-libdir --merge-multiarch csaw_1.6.1.tar.gz && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL csaw_1.6.1.zip && rm csaw_1.6.1.tar.gz csaw_1.6.1.zip
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install for i386
* installing *source* package 'csaw' ...
** libs
C:/Rtools/mingw_32/bin/g++ -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.3-bioc/R/library/Rhtslib/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c annotator.cpp -o annotator.o
C:/Rtools/mingw_32/bin/g++ -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.3-bioc/R/library/Rhtslib/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c bam_utils.cpp -o bam_utils.o
C:/Rtools/mingw_32/bin/g++ -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.3-bioc/R/library/Rhtslib/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c best_in_cluster.cpp -o best_in_cluster.o
C:/Rtools/mingw_32/bin/g++ -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.3-bioc/R/library/Rhtslib/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c check_bimodality.cpp -o check_bimodality.o
C:/Rtools/mingw_32/bin/g++ -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.3-bioc/R/library/Rhtslib/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c correlate_reads.cpp -o correlate_reads.o
C:/Rtools/mingw_32/bin/g++ -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.3-bioc/R/library/Rhtslib/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c find_maxima.cpp -o find_maxima.o
find_maxima.cpp: In function 'SEXPREC* find_maxima(SEXP, SEXP, SEXP, SEXP, SEXP)':
find_maxima.cpp:90:4: warning: 'is_max' may be used uninitialized in this function [-Wmaybe-uninitialized]
while (right_copy >= is_max) {
^
C:/Rtools/mingw_32/bin/g++ -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.3-bioc/R/library/Rhtslib/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c get_cluster_stats.cpp -o get_cluster_stats.o
C:/Rtools/mingw_32/bin/g++ -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.3-bioc/R/library/Rhtslib/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c get_profile.cpp -o get_profile.o
C:/Rtools/mingw_32/bin/g++ -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.3-bioc/R/library/Rhtslib/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c get_rle_counts.cpp -o get_rle_counts.o
C:/Rtools/mingw_32/bin/g++ -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.3-bioc/R/library/Rhtslib/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c init.cpp -o init.o
C:/Rtools/mingw_32/bin/g++ -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.3-bioc/R/library/Rhtslib/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c merge_windows.cpp -o merge_windows.o
C:/Rtools/mingw_32/bin/g++ -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.3-bioc/R/library/Rhtslib/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c pair_reads.cpp -o pair_reads.o
C:/Rtools/mingw_32/bin/g++ -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.3-bioc/R/library/Rhtslib/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c single_reads.cpp -o single_reads.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o csaw.dll tmp.def annotator.o bam_utils.o best_in_cluster.o check_bimodality.o correlate_reads.o find_maxima.o get_cluster_stats.o get_profile.o get_rle_counts.o init.o merge_windows.o pair_reads.o single_reads.o -LE:/biocbld/bbs-3.3-bioc/R/library/Rhtslib/lib/i386 -lhts -lz -pthread -lws2_32 -Lc:/local323/lib/i386 -Lc:/local323/lib -LE:/biocbld/BBS-3˜1.3-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-3.3-bioc/meat/csaw.buildbin-libdir/csaw/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
'csaw.Rnw'
** testing if installed package can be loaded
install for x64
* installing *source* package 'csaw' ...
** libs
C:/Rtools/mingw_64/bin/g++ -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.3-bioc/R/library/Rhtslib/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c annotator.cpp -o annotator.o
C:/Rtools/mingw_64/bin/g++ -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.3-bioc/R/library/Rhtslib/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c bam_utils.cpp -o bam_utils.o
C:/Rtools/mingw_64/bin/g++ -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.3-bioc/R/library/Rhtslib/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c best_in_cluster.cpp -o best_in_cluster.o
C:/Rtools/mingw_64/bin/g++ -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.3-bioc/R/library/Rhtslib/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c check_bimodality.cpp -o check_bimodality.o
C:/Rtools/mingw_64/bin/g++ -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.3-bioc/R/library/Rhtslib/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c correlate_reads.cpp -o correlate_reads.o
C:/Rtools/mingw_64/bin/g++ -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.3-bioc/R/library/Rhtslib/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c find_maxima.cpp -o find_maxima.o
find_maxima.cpp: In function 'SEXPREC* find_maxima(SEXP, SEXP, SEXP, SEXP, SEXP)':
find_maxima.cpp:90:4: warning: 'is_max' may be used uninitialized in this function [-Wmaybe-uninitialized]
while (right_copy >= is_max) {
^
C:/Rtools/mingw_64/bin/g++ -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.3-bioc/R/library/Rhtslib/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c get_cluster_stats.cpp -o get_cluster_stats.o
C:/Rtools/mingw_64/bin/g++ -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.3-bioc/R/library/Rhtslib/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c get_profile.cpp -o get_profile.o
C:/Rtools/mingw_64/bin/g++ -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.3-bioc/R/library/Rhtslib/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c get_rle_counts.cpp -o get_rle_counts.o
C:/Rtools/mingw_64/bin/g++ -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.3-bioc/R/library/Rhtslib/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c init.cpp -o init.o
C:/Rtools/mingw_64/bin/g++ -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.3-bioc/R/library/Rhtslib/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c merge_windows.cpp -o merge_windows.o
C:/Rtools/mingw_64/bin/g++ -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.3-bioc/R/library/Rhtslib/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c pair_reads.cpp -o pair_reads.o
C:/Rtools/mingw_64/bin/g++ -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -I"E:/biocbld/bbs-3.3-bioc/R/library/Rhtslib/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/local323/include" -O2 -Wall -mtune=core2 -c single_reads.cpp -o single_reads.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o csaw.dll tmp.def annotator.o bam_utils.o best_in_cluster.o check_bimodality.o correlate_reads.o find_maxima.o get_cluster_stats.o get_profile.o get_rle_counts.o init.o merge_windows.o pair_reads.o single_reads.o -LE:/biocbld/bbs-3.3-bioc/R/library/Rhtslib/lib/x64 -lhts -lz -pthread -lws2_32 -Lc:/local323/lib/x64 -Lc:/local323/lib -LE:/biocbld/BBS-3˜1.3-B/R/bin/x64 -lR
installing to E:/biocbld/bbs-3.3-bioc/meat/csaw.buildbin-libdir/csaw/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'csaw' as csaw_1.6.1.zip
* DONE (csaw)
* installing to library 'E:/biocbld/bbs-3.3-bioc/R/library'
package 'csaw' successfully unpacked and MD5 sums checked