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BioC 3.3: INSTALL report for oligo on moscato2

This page was generated on 2016-10-13 12:47:36 -0700 (Thu, 13 Oct 2016).

Package 798/1210HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
oligo 1.36.1
Benilton Carvalho
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/oligo
Last Changed Rev: 117513 / Revision: 122332
Last Changed Date: 2016-05-15 13:18:19 -0700 (Sun, 15 May 2016)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 [ OK ] OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: oligo
Version: 1.36.1
Command: rm -rf oligo.buildbin-libdir && mkdir oligo.buildbin-libdir && C:\cygwin\bin\curl.exe -O http://zin2/BBS/3.3/bioc/src/contrib/oligo_1.36.1.tar.gz && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --library=oligo.buildbin-libdir --merge-multiarch oligo_1.36.1.tar.gz && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL oligo_1.36.1.zip && rm oligo_1.36.1.tar.gz oligo_1.36.1.zip
StartedAt: 2016-10-12 18:57:47 -0700 (Wed, 12 Oct 2016)
EndedAt: 2016-10-12 18:59:41 -0700 (Wed, 12 Oct 2016)
EllapsedTime: 113.5 seconds
RetCode: 0
Status:  OK  

Command output

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###
### Running command:
###
###   rm -rf oligo.buildbin-libdir && mkdir oligo.buildbin-libdir  && C:\cygwin\bin\curl.exe -O http://zin2/BBS/3.3/bioc/src/contrib/oligo_1.36.1.tar.gz && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --library=oligo.buildbin-libdir --merge-multiarch oligo_1.36.1.tar.gz && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL oligo_1.36.1.zip  && rm oligo_1.36.1.tar.gz oligo_1.36.1.zip
###
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install for i386

* installing *source* package 'oligo' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/preprocessCore/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c DABG.c -o DABG.o
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/preprocessCore/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c ParserGzXYS.c -o ParserGzXYS.o
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/preprocessCore/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c ParserXYS.c -o ParserXYS.o
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/preprocessCore/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c baseProfile.c -o baseProfile.o
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/preprocessCore/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c basecontent.c -o basecontent.o
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/preprocessCore/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c chipbackground.c -o chipbackground.o
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/preprocessCore/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c mas5calls.c -o mas5calls.o
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/preprocessCore/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c rma2.c -o rma2.o
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/preprocessCore/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c rma_common.c -o rma_common.o
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/preprocessCore/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c trimmed.c -o trimmed.o
C:/Rtools/mingw_32/bin/gcc -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 -LE:/biocbld/BBS-3˜1.3-B/R/bin/i386 -lRlapack -LE:/biocbld/BBS-3˜1.3-B/R/bin/i386 -lRblas -LE:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -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/oligo.buildbin-libdir/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 *source* package 'oligo' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/preprocessCore/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c DABG.c -o DABG.o
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/preprocessCore/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c ParserGzXYS.c -o ParserGzXYS.o
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/preprocessCore/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c ParserXYS.c -o ParserXYS.o
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/preprocessCore/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c baseProfile.c -o baseProfile.o
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/preprocessCore/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c basecontent.c -o basecontent.o
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/preprocessCore/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c chipbackground.c -o chipbackground.o
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/preprocessCore/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c mas5calls.c -o mas5calls.o
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/preprocessCore/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c rma2.c -o rma2.o
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/preprocessCore/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c rma_common.c -o rma_common.o
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/preprocessCore/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c trimmed.c -o trimmed.o
C:/Rtools/mingw_64/bin/gcc -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 -LE:/biocbld/BBS-3˜1.3-B/R/bin/x64 -lRlapack -LE:/biocbld/BBS-3˜1.3-B/R/bin/x64 -lRblas -LE:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -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/oligo.buildbin-libdir/oligo/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'oligo' as oligo_1.36.1.zip
* DONE (oligo)
* installing to library 'E:/biocbld/bbs-3.3-bioc/R/library'
package 'oligo' successfully unpacked and MD5 sums checked