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BioC 3.3: INSTALL report for edgeR on moscato2

This page was generated on 2016-10-13 12:48:41 -0700 (Thu, 13 Oct 2016).

Package 340/1210HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
edgeR 3.14.0
Yunshun Chen , Aaron Lun , Mark Robinson , Davis McCarthy , Gordon Smyth
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/edgeR
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  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 [ OK ] OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: edgeR
Version: 3.14.0
Command: rm -rf edgeR.buildbin-libdir && mkdir edgeR.buildbin-libdir && C:\cygwin\bin\curl.exe -O http://zin2/BBS/3.3/bioc/src/contrib/edgeR_3.14.0.tar.gz && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --library=edgeR.buildbin-libdir --merge-multiarch edgeR_3.14.0.tar.gz && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL edgeR_3.14.0.zip && rm edgeR_3.14.0.tar.gz edgeR_3.14.0.zip
StartedAt: 2016-10-12 18:32:24 -0700 (Wed, 12 Oct 2016)
EndedAt: 2016-10-12 18:34:12 -0700 (Wed, 12 Oct 2016)
EllapsedTime: 108.5 seconds
RetCode: 0
Status:  OK  

Command output

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###
### Running command:
###
###   rm -rf edgeR.buildbin-libdir && mkdir edgeR.buildbin-libdir  && C:\cygwin\bin\curl.exe -O http://zin2/BBS/3.3/bioc/src/contrib/edgeR_3.14.0.tar.gz && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --library=edgeR.buildbin-libdir --merge-multiarch edgeR_3.14.0.tar.gz && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL edgeR_3.14.0.zip  && rm edgeR_3.14.0.tar.gz edgeR_3.14.0.zip
###
##############################################################################
##############################################################################




install for i386

* installing *source* package 'edgeR' ...
** libs
C:/Rtools/mingw_32/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c R_compute_nbdev.cpp -o R_compute_nbdev.o
C:/Rtools/mingw_32/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c R_cr_adjust.cpp -o R_cr_adjust.o
C:/Rtools/mingw_32/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c R_exact_test_by_deviance.cpp -o R_exact_test_by_deviance.o
C:/Rtools/mingw_32/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c R_levenberg.cpp -o R_levenberg.o
C:/Rtools/mingw_32/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c R_loess_by_col.cpp -o R_loess_by_col.o
C:/Rtools/mingw_32/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c R_maximize_interpolant.cpp -o R_maximize_interpolant.o
C:/Rtools/mingw_32/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c R_one_group.cpp -o R_one_group.o
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c R_process_hairpin_reads.c -o R_process_hairpin_reads.o
C:/Rtools/mingw_32/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c R_simple_good_turing.cpp -o R_simple_good_turing.o
C:/Rtools/mingw_32/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c adj_coxreid.cpp -o adj_coxreid.o
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c fmm_spline.c -o fmm_spline.o
C:/Rtools/mingw_32/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c glm_levenberg.cpp -o glm_levenberg.o
C:/Rtools/mingw_32/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c glm_one_group.cpp -o glm_one_group.o
C:/Rtools/mingw_32/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -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"c:/local323/include"     -O2 -Wall  -mtune=core2 -c interpolator.cpp -o interpolator.o
C:/Rtools/mingw_32/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c matvec_check.cpp -o matvec_check.o
C:/Rtools/mingw_32/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c nbdev.cpp -o nbdev.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o edgeR.dll tmp.def R_compute_nbdev.o R_cr_adjust.o R_exact_test_by_deviance.o R_levenberg.o R_loess_by_col.o R_maximize_interpolant.o R_one_group.o R_process_hairpin_reads.o R_simple_good_turing.o adj_coxreid.o fmm_spline.o glm_levenberg.o glm_one_group.o init.o interpolator.o matvec_check.o nbdev.o -LE:/biocbld/BBS-3˜1.3-B/R/bin/i386 -lRlapack -LE:/biocbld/BBS-3˜1.3-B/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -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/edgeR.buildbin-libdir/edgeR/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'edgeR.Rnw' 
** testing if installed package can be loaded

install for x64

* installing *source* package 'edgeR' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c R_compute_nbdev.cpp -o R_compute_nbdev.o
C:/Rtools/mingw_64/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c R_cr_adjust.cpp -o R_cr_adjust.o
C:/Rtools/mingw_64/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c R_exact_test_by_deviance.cpp -o R_exact_test_by_deviance.o
C:/Rtools/mingw_64/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c R_levenberg.cpp -o R_levenberg.o
C:/Rtools/mingw_64/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c R_loess_by_col.cpp -o R_loess_by_col.o
C:/Rtools/mingw_64/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c R_maximize_interpolant.cpp -o R_maximize_interpolant.o
C:/Rtools/mingw_64/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c R_one_group.cpp -o R_one_group.o
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c R_process_hairpin_reads.c -o R_process_hairpin_reads.o
C:/Rtools/mingw_64/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c R_simple_good_turing.cpp -o R_simple_good_turing.o
C:/Rtools/mingw_64/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c adj_coxreid.cpp -o adj_coxreid.o
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c fmm_spline.c -o fmm_spline.o
C:/Rtools/mingw_64/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c glm_levenberg.cpp -o glm_levenberg.o
C:/Rtools/mingw_64/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c glm_one_group.cpp -o glm_one_group.o
C:/Rtools/mingw_64/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -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"c:/local323/include"     -O2 -Wall  -mtune=core2 -c interpolator.cpp -o interpolator.o
C:/Rtools/mingw_64/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c matvec_check.cpp -o matvec_check.o
C:/Rtools/mingw_64/bin/g++  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG     -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c nbdev.cpp -o nbdev.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o edgeR.dll tmp.def R_compute_nbdev.o R_cr_adjust.o R_exact_test_by_deviance.o R_levenberg.o R_loess_by_col.o R_maximize_interpolant.o R_one_group.o R_process_hairpin_reads.o R_simple_good_turing.o adj_coxreid.o fmm_spline.o glm_levenberg.o glm_one_group.o init.o interpolator.o matvec_check.o nbdev.o -LE:/biocbld/BBS-3˜1.3-B/R/bin/x64 -lRlapack -LE:/biocbld/BBS-3˜1.3-B/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -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/edgeR.buildbin-libdir/edgeR/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'edgeR' as edgeR_3.14.0.zip
* DONE (edgeR)
* installing to library 'E:/biocbld/bbs-3.3-bioc/R/library'
package 'edgeR' successfully unpacked and MD5 sums checked