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BioC 3.4: INSTALL report for edgeR on moscato1

This page was generated on 2016-09-21 03:42:35 -0700 (Wed, 21 Sep 2016).

Package 358/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
edgeR 3.15.2
Yunshun Chen , Aaron Lun , Mark Robinson , Davis McCarthy , Gordon Smyth
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/edgeR
Last Changed Rev: 119042 / Revision: 121152
Last Changed Date: 2016-06-29 18:47:59 -0700 (Wed, 29 Jun 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: edgeR
Version: 3.15.2
Command: rm -rf edgeR.buildbin-libdir && mkdir edgeR.buildbin-libdir && C:\cygwin\bin\curl.exe -O http://zin1/BBS/3.4/bioc/src/contrib/edgeR_3.15.2.tar.gz && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --library=edgeR.buildbin-libdir --merge-multiarch edgeR_3.15.2.tar.gz && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL edgeR_3.15.2.zip && rm edgeR_3.15.2.tar.gz edgeR_3.15.2.zip
StartedAt: 2016-09-19 20:30:16 -0700 (Mon, 19 Sep 2016)
EndedAt: 2016-09-19 20:31:21 -0700 (Mon, 19 Sep 2016)
EllapsedTime: 65.7 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://zin1/BBS/3.4/bioc/src/contrib/edgeR_3.15.2.tar.gz && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --library=edgeR.buildbin-libdir --merge-multiarch edgeR_3.15.2.tar.gz && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL edgeR_3.15.2.zip  && rm edgeR_3.15.2.tar.gz edgeR_3.15.2.zip
###
##############################################################################
##############################################################################


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  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1298k  100 1298k    0     0  54.5M      0 --:--:-- --:--:-- --:--:-- 66.7M

install for i386

* installing *source* package 'edgeR' ...
** libs
C:/Rtools/mingw_32/bin/g++  -I"D:/biocbld/BBS-3˜1.4-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"D:/biocbld/BBS-3˜1.4-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"D:/biocbld/BBS-3˜1.4-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"D:/biocbld/BBS-3˜1.4-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"D:/biocbld/BBS-3˜1.4-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"D:/biocbld/BBS-3˜1.4-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"D:/biocbld/BBS-3˜1.4-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"D:/biocbld/BBS-3˜1.4-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"D:/biocbld/BBS-3˜1.4-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"D:/biocbld/BBS-3˜1.4-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"D:/biocbld/BBS-3˜1.4-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"D:/biocbld/BBS-3˜1.4-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"D:/biocbld/BBS-3˜1.4-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"D:/biocbld/BBS-3˜1.4-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"D:/biocbld/BBS-3˜1.4-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"D:/biocbld/BBS-3˜1.4-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"D:/biocbld/BBS-3˜1.4-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 -LD:/biocbld/BBS-3˜1.4-B/R/bin/i386 -lRlapack -LD:/biocbld/BBS-3˜1.4-B/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -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/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"D:/biocbld/BBS-3˜1.4-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"D:/biocbld/BBS-3˜1.4-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"D:/biocbld/BBS-3˜1.4-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"D:/biocbld/BBS-3˜1.4-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"D:/biocbld/BBS-3˜1.4-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"D:/biocbld/BBS-3˜1.4-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"D:/biocbld/BBS-3˜1.4-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"D:/biocbld/BBS-3˜1.4-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"D:/biocbld/BBS-3˜1.4-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"D:/biocbld/BBS-3˜1.4-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"D:/biocbld/BBS-3˜1.4-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"D:/biocbld/BBS-3˜1.4-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"D:/biocbld/BBS-3˜1.4-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"D:/biocbld/BBS-3˜1.4-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"D:/biocbld/BBS-3˜1.4-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"D:/biocbld/BBS-3˜1.4-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"D:/biocbld/BBS-3˜1.4-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 -LD:/biocbld/BBS-3˜1.4-B/R/bin/x64 -lRlapack -LD:/biocbld/BBS-3˜1.4-B/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -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/edgeR.buildbin-libdir/edgeR/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'edgeR' as edgeR_3.15.2.zip
* DONE (edgeR)
* installing to library 'D:/biocbld/bbs-3.4-bioc/R/library'
package 'edgeR' successfully unpacked and MD5 sums checked