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BioC 3.3: INSTALL report for oligo on windows2.bioconductor.org

This page was generated on 2015-10-27 12:14:03 -0400 (Tue, 27 Oct 2015).

Package 721/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
oligo 1.35.0
Benilton Carvalho
Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo
Last Changed Rev: 109592 / Revision: 109948
Last Changed Date: 2015-10-13 15:59:53 -0400 (Tue, 13 Oct 2015)
linux2.bioconductor.org Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
windows2.bioconductor.org Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 [ OK ] OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: oligo
Version: 1.35.0
Command: C:\cygwin64\bin\curl.exe -O http://linux2.bioconductor.org/BBS/3.3/bioc/src/contrib/oligo_1.35.0.tar.gz && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch oligo_1.35.0.tar.gz && rm oligo_1.35.0.tar.gz
StartedAt: 2015-10-26 21:09:25 -0400 (Mon, 26 Oct 2015)
EndedAt: 2015-10-26 21:09:52 -0400 (Mon, 26 Oct 2015)
EllapsedTime: 26.5 seconds
RetCode: 0
Status:  OK  

Command output

##############################################################################
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###
### Running command:
###
###   C:\cygwin64\bin\curl.exe -O http://linux2.bioconductor.org/BBS/3.3/bioc/src/contrib/oligo_1.35.0.tar.gz && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch oligo_1.35.0.tar.gz && rm oligo_1.35.0.tar.gz
###
##############################################################################
##############################################################################


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100 14.9M  100 14.9M    0     0   236M      0 --:--:-- --:--:-- --:--:--  248M

install for i386

* installing to library 'c:/biocbld/bbs-3.3-bioc/R/library'
* installing *source* package 'oligo' ...
** libs
gcc -m32 -I"C:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"c:/biocbld/bbs-3.3-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c DABG.c -o DABG.o
gcc -m32 -I"C:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"c:/biocbld/bbs-3.3-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c ParserGzXYS.c -o ParserGzXYS.o
gcc -m32 -I"C:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"c:/biocbld/bbs-3.3-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c ParserXYS.c -o ParserXYS.o
gcc -m32 -I"C:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"c:/biocbld/bbs-3.3-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c baseProfile.c -o baseProfile.o
gcc -m32 -I"C:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"c:/biocbld/bbs-3.3-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c basecontent.c -o basecontent.o
gcc -m32 -I"C:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"c:/biocbld/bbs-3.3-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c chipbackground.c -o chipbackground.o
gcc -m32 -I"C:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"c:/biocbld/bbs-3.3-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c mas5calls.c -o mas5calls.o
gcc -m32 -I"C:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"c:/biocbld/bbs-3.3-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c rma2.c -o rma2.o
gcc -m32 -I"C:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"c:/biocbld/bbs-3.3-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c rma_common.c -o rma_common.o
gcc -m32 -I"C:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"c:/biocbld/bbs-3.3-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c trimmed.c -o trimmed.o
gcc -m32 -shared -s -static-libgcc -o oligo.dll tmp.def DABG.o ParserGzXYS.o ParserXYS.o baseProfile.o basecontent.o chipbackground.o mas5calls.o rma2.o rma_common.o trimmed.o -lgfortran -lm -lquadmath -Lc:/biocbld/BBS-3˜1.3-B/R/bin/i386 -lRlapack -Lc:/biocbld/BBS-3˜1.3-B/R/bin/i386 -lRblas -LC:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -Ld:/RCompile/r-compiling/local/local320/lib/i386 -Ld:/RCompile/r-compiling/local/local320/lib -Lc:/biocbld/BBS-3˜1.3-B/R/bin/i386 -lR
installing to c:/biocbld/bbs-3.3-bioc/R/library/oligo/libs/i386
** R
** inst
** preparing package for lazy loading
Note: in method for 'pm<-' with signature
'object="TilingFeatureSet",subset="ANY",target="ANY",value="array"':
expanding the signature to include omitted arguments in definition: =
"missing"
Note: in method for 'mm<-' with signature
'object="TilingFeatureSet",subset="ANY",target="ANY",value="array"':
expanding the signature to include omitted arguments in definition: =
"missing"
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing to library 'c:/biocbld/bbs-3.3-bioc/R/library'
* installing *source* package 'oligo' ...
** libs
gcc -m64 -I"C:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"c:/biocbld/bbs-3.3-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c DABG.c -o DABG.o
gcc -m64 -I"C:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"c:/biocbld/bbs-3.3-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c ParserGzXYS.c -o ParserGzXYS.o
gcc -m64 -I"C:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"c:/biocbld/bbs-3.3-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c ParserXYS.c -o ParserXYS.o
gcc -m64 -I"C:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"c:/biocbld/bbs-3.3-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c baseProfile.c -o baseProfile.o
gcc -m64 -I"C:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"c:/biocbld/bbs-3.3-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c basecontent.c -o basecontent.o
gcc -m64 -I"C:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"c:/biocbld/bbs-3.3-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c chipbackground.c -o chipbackground.o
gcc -m64 -I"C:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"c:/biocbld/bbs-3.3-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c mas5calls.c -o mas5calls.o
gcc -m64 -I"C:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"c:/biocbld/bbs-3.3-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c rma2.c -o rma2.o
gcc -m64 -I"C:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"c:/biocbld/bbs-3.3-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c rma_common.c -o rma_common.o
gcc -m64 -I"C:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"c:/biocbld/bbs-3.3-bioc/R/library/preprocessCore/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c trimmed.c -o trimmed.o
gcc -m64 -shared -s -static-libgcc -o oligo.dll tmp.def DABG.o ParserGzXYS.o ParserXYS.o baseProfile.o basecontent.o chipbackground.o mas5calls.o rma2.o rma_common.o trimmed.o -lgfortran -lm -lquadmath -Lc:/biocbld/BBS-3˜1.3-B/R/bin/x64 -lRlapack -Lc:/biocbld/BBS-3˜1.3-B/R/bin/x64 -lRblas -LC:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -Ld:/RCompile/r-compiling/local/local320/lib/x64 -Ld:/RCompile/r-compiling/local/local320/lib -Lc:/biocbld/BBS-3˜1.3-B/R/bin/x64 -lR
installing to c:/biocbld/bbs-3.3-bioc/R/library/oligo/libs/x64
** testing if installed package can be loaded
* DONE (oligo)