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BioC 3.4: INSTALL report for csaw on moscato1

This page was generated on 2016-09-21 03:46:26 -0700 (Wed, 21 Sep 2016).

Package 275/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
csaw 1.7.3
Aaron Lun
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/csaw
Last Changed Rev: 120207 / Revision: 121152
Last Changed Date: 2016-08-17 03:17:05 -0700 (Wed, 17 Aug 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64 [ OK ] OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: csaw
Version: 1.7.3
Command: rm -rf csaw.buildbin-libdir && mkdir csaw.buildbin-libdir && C:\cygwin\bin\curl.exe -O http://zin1/BBS/3.4/bioc/src/contrib/csaw_1.7.3.tar.gz && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --library=csaw.buildbin-libdir --merge-multiarch csaw_1.7.3.tar.gz && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL csaw_1.7.3.zip && rm csaw_1.7.3.tar.gz csaw_1.7.3.zip
StartedAt: 2016-09-19 21:07:30 -0700 (Mon, 19 Sep 2016)
EndedAt: 2016-09-19 21:08:49 -0700 (Mon, 19 Sep 2016)
EllapsedTime: 79.2 seconds
RetCode: 0
Status:  OK  

Command output

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###
### Running command:
###
###   rm -rf csaw.buildbin-libdir && mkdir csaw.buildbin-libdir  && C:\cygwin\bin\curl.exe -O http://zin1/BBS/3.4/bioc/src/contrib/csaw_1.7.3.tar.gz && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --library=csaw.buildbin-libdir --merge-multiarch csaw_1.7.3.tar.gz && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL csaw_1.7.3.zip  && rm csaw_1.7.3.tar.gz csaw_1.7.3.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1340k  100 1340k    0     0  42.1M      0 --:--:-- --:--:-- --:--:-- 54.5M

install for i386

* installing *source* package 'csaw' ...
** libs
C:/Rtools/mingw_32/bin/g++  -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rhtslib/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rhtslib/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rhtslib/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rhtslib/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rhtslib/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rhtslib/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rhtslib/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rhtslib/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rhtslib/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rhtslib/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rhtslib/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rhtslib/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rhtslib/include" -I"D:/biocbld/bbs-3.4-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 -LD:/biocbld/bbs-3.4-bioc/R/library/Rhtslib/lib/i386 -lhts -lz -pthread -lws2_32 -Lc:/local323/lib/i386 -Lc:/local323/lib -LD:/biocbld/BBS-3˜1.4-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rhtslib/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rhtslib/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rhtslib/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rhtslib/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rhtslib/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rhtslib/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rhtslib/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rhtslib/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rhtslib/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rhtslib/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rhtslib/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rhtslib/include" -I"D:/biocbld/bbs-3.4-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"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/Rhtslib/include" -I"D:/biocbld/bbs-3.4-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 -LD:/biocbld/bbs-3.4-bioc/R/library/Rhtslib/lib/x64 -lhts -lz -pthread -lws2_32 -Lc:/local323/lib/x64 -Lc:/local323/lib -LD:/biocbld/BBS-3˜1.4-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-3.4-bioc/meat/csaw.buildbin-libdir/csaw/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'csaw' as csaw_1.7.3.zip
* DONE (csaw)
* installing to library 'D:/biocbld/bbs-3.4-bioc/R/library'
package 'csaw' successfully unpacked and MD5 sums checked