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Package 156/609HostnameOS / ArchBUILDCHECKBUILD BIN
DECIPHER 1.4.0
Erik Wright
Snapshot Date: 2013-03-24 16:21:20 -0700 (Sun, 24 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_11/madman/Rpacks/DECIPHER
Last Changed Rev: 70050 / Revision: 74773
Last Changed Date: 2012-10-01 15:16:24 -0700 (Mon, 01 Oct 2012)
lamb1 Linux (openSUSE 12.1) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK [ OK ]
perceval Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: DECIPHER
Version: 1.4.0
Command: rm -rf DECIPHER.buildbin-libdir && mkdir DECIPHER.buildbin-libdir && D:\biocbld\bbs-2.11-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=DECIPHER.buildbin-libdir DECIPHER_1.4.0.tar.gz
StartedAt: 2013-03-25 03:52:37 -0700 (Mon, 25 Mar 2013)
EndedAt: 2013-03-25 03:53:19 -0700 (Mon, 25 Mar 2013)
EllapsedTime: 42.1 seconds
RetCode: 0
Status:  OK  
PackageFile: DECIPHER_1.4.0.zip
PackageFileSize: 1.208 MiB

Command output


install for i386

* installing *source* package 'DECIPHER' ...
** libs
gcc -m32 -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/RSQLite/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/stats/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=core2 -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -m32 -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/RSQLite/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/stats/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=core2 -c CalculateDeltaG.c -o CalculateDeltaG.o
CalculateDeltaG.c: In function 'calculateDeltaG':
CalculateDeltaG.c:26:10: warning: 's2' may be used uninitialized in this function [-Wuninitialized]
CalculateDeltaG.c:206:15: warning: 's1' may be used uninitialized in this function [-Wuninitialized]
gcc -m32 -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/RSQLite/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/stats/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=core2 -c ClusterML.c -o ClusterML.o
gcc -m32 -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/RSQLite/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/stats/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=core2 -c ClusterNJ.c -o ClusterNJ.o
ClusterNJ.c: In function 'clusterNJ._omp_fn.0':
ClusterNJ.c:195:62: warning: 'minC' may be used uninitialized in this function [-Wuninitialized]
ClusterNJ.c:195:56: warning: 'minR' may be used uninitialized in this function [-Wuninitialized]
gcc -m32 -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/RSQLite/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/stats/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=core2 -c ClusterUPGMA.c -o ClusterUPGMA.o
ClusterUPGMA.c: In function 'clusterUPGMA._omp_fn.0':
ClusterUPGMA.c:124:62: warning: 'minC' may be used uninitialized in this function [-Wuninitialized]
ClusterUPGMA.c:124:56: warning: 'minR' may be used uninitialized in this function [-Wuninitialized]
gcc -m32 -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/RSQLite/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/stats/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=core2 -c CommonGaps.c -o CommonGaps.o
gcc -m32 -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/RSQLite/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/stats/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=core2 -c ConsensusSequence.c -o ConsensusSequence.o
gcc -m32 -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/RSQLite/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/stats/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=core2 -c DistanceMatrix.c -o DistanceMatrix.o
gcc -m32 -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/RSQLite/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/stats/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=core2 -c MultiMatch.c -o MultiMatch.o
gcc -m32 -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/RSQLite/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/stats/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=core2 -c R_init_decipher.c -o R_init_decipher.o
gcc -m32 -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/RSQLite/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/stats/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=core2 -c ReplaceChars.c -o ReplaceChars.o
gcc -m32 -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/RSQLite/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/stats/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp   -O3 -Wall  -std=gnu99 -mtune=core2 -c TerminalMismatch.c -o TerminalMismatch.o
gcc -m32 -shared -s -static-libgcc -o DECIPHER.dll tmp.def Biostrings_stubs.o CalculateDeltaG.o ClusterML.o ClusterNJ.o ClusterUPGMA.o CommonGaps.o ConsensusSequence.o DistanceMatrix.o MultiMatch.o R_init_decipher.o ReplaceChars.o TerminalMismatch.o -fopenmp -Ld:/RCompile/CRANpkg/extralibs64/local/lib/i386 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LD:/biocbld/BBS-2˜1.11-/R/bin/i386 -lR
installing to D:/biocbld/bbs-2.11-bioc/meat/DECIPHER.buildbin-libdir/DECIPHER/libs/i386
** R
** data
**  moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'DECIPHERing.Rnw' 
   'DesignPrimers.Rnw' 
   'FindChimeras.Rnw' 
** testing if installed package can be loaded

install for x64

* installing *source* package 'DECIPHER' ...
** libs
gcc -m64 -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/RSQLite/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/stats/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=core2 -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/RSQLite/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/stats/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=core2 -c CalculateDeltaG.c -o CalculateDeltaG.o
CalculateDeltaG.c: In function 'calculateDeltaG':
CalculateDeltaG.c:26:10: warning: 's2' may be used uninitialized in this function [-Wuninitialized]
CalculateDeltaG.c:206:15: warning: 's1' may be used uninitialized in this function [-Wuninitialized]
gcc -m64 -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/RSQLite/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/stats/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=core2 -c ClusterML.c -o ClusterML.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/RSQLite/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/stats/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=core2 -c ClusterNJ.c -o ClusterNJ.o
ClusterNJ.c: In function 'clusterNJ._omp_fn.0':
ClusterNJ.c:280:12: warning: 'minC' may be used uninitialized in this function [-Wuninitialized]
ClusterNJ.c:195:62: note: 'minC' was declared here
ClusterNJ.c:279:12: warning: 'minR' may be used uninitialized in this function [-Wuninitialized]
ClusterNJ.c:195:56: note: 'minR' was declared here
gcc -m64 -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/RSQLite/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/stats/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=core2 -c ClusterUPGMA.c -o ClusterUPGMA.o
ClusterUPGMA.c: In function 'clusterUPGMA._omp_fn.0':
ClusterUPGMA.c:197:12: warning: 'minC' may be used uninitialized in this function [-Wuninitialized]
ClusterUPGMA.c:124:62: note: 'minC' was declared here
ClusterUPGMA.c:196:12: warning: 'minR' may be used uninitialized in this function [-Wuninitialized]
ClusterUPGMA.c:124:56: note: 'minR' was declared here
gcc -m64 -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/RSQLite/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/stats/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=core2 -c CommonGaps.c -o CommonGaps.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/RSQLite/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/stats/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=core2 -c ConsensusSequence.c -o ConsensusSequence.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/RSQLite/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/stats/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=core2 -c DistanceMatrix.c -o DistanceMatrix.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/RSQLite/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/stats/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=core2 -c MultiMatch.c -o MultiMatch.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/RSQLite/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/stats/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=core2 -c R_init_decipher.c -o R_init_decipher.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/RSQLite/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/stats/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=core2 -c ReplaceChars.c -o ReplaceChars.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/RSQLite/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/stats/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=core2 -c TerminalMismatch.c -o TerminalMismatch.o
gcc -m64 -shared -s -static-libgcc -o DECIPHER.dll tmp.def Biostrings_stubs.o CalculateDeltaG.o ClusterML.o ClusterNJ.o ClusterUPGMA.o CommonGaps.o ConsensusSequence.o DistanceMatrix.o MultiMatch.o R_init_decipher.o ReplaceChars.o TerminalMismatch.o -fopenmp -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LD:/biocbld/BBS-2˜1.11-/R/bin/x64 -lR
installing to D:/biocbld/bbs-2.11-bioc/meat/DECIPHER.buildbin-libdir/DECIPHER/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DECIPHER' as DECIPHER_1.4.0.zip

* DONE (DECIPHER)