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Package 142/553HostnameOS / ArchBUILDCHECKBUILD BIN
DECIPHER 1.2.0
Erik Wright
Snapshot Date: 2012-09-23 17:01:39 -0700 (Sun, 23 Sep 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_10/madman/Rpacks/DECIPHER
Last Changed Rev: 64678 / Revision: 69725
Last Changed Date: 2012-03-30 15:05:02 -0700 (Fri, 30 Mar 2012)
lamb2 Linux (openSUSE 11.4) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK [ OK ]
petty Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: DECIPHER
Version: 1.2.0
Command: rm -rf DECIPHER.buildbin-libdir && mkdir DECIPHER.buildbin-libdir && E:\biocbld\bbs-2.10-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=DECIPHER.buildbin-libdir DECIPHER_1.2.0.tar.gz
StartedAt: 2012-09-24 03:05:25 -0700 (Mon, 24 Sep 2012)
EndedAt: 2012-09-24 03:05:52 -0700 (Mon, 24 Sep 2012)
EllapsedTime: 26.3 seconds
RetCode: 0
Status:  OK  
PackageFile: DECIPHER_1.2.0.zip
PackageFileSize: 834.6 KiB

Command output


install for i386

* installing *source* package 'DECIPHER' ...
** libs
gcc  -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.10-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/RSQLite/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/stats/include"   -fopenmp   -O3 -Wall  -std=gnu99 -mtune=core2 -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc  -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.10-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/RSQLite/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/stats/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  -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.10-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/RSQLite/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/stats/include"   -fopenmp   -O3 -Wall  -std=gnu99 -mtune=core2 -c ClusterML.c -o ClusterML.o
gcc  -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.10-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/RSQLite/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/stats/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  -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.10-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/RSQLite/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/stats/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  -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.10-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/RSQLite/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/stats/include"   -fopenmp   -O3 -Wall  -std=gnu99 -mtune=core2 -c CommonGaps.c -o CommonGaps.o
gcc  -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.10-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/RSQLite/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/stats/include"   -fopenmp   -O3 -Wall  -std=gnu99 -mtune=core2 -c ConsensusSequence.c -o ConsensusSequence.o
gcc  -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.10-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/RSQLite/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/stats/include"   -fopenmp   -O3 -Wall  -std=gnu99 -mtune=core2 -c DistanceMatrix.c -o DistanceMatrix.o
gcc  -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.10-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/RSQLite/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/stats/include"   -fopenmp   -O3 -Wall  -std=gnu99 -mtune=core2 -c R_init_decipher.c -o R_init_decipher.o
gcc  -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.10-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/RSQLite/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/stats/include"   -fopenmp   -O3 -Wall  -std=gnu99 -mtune=core2 -c ReplaceChars.c -o ReplaceChars.o
gcc -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 R_init_decipher.o ReplaceChars.o -fopenmp -LE:/biocbld/BBS-2~1.10-/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.10-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' 
   'FindChimeras.Rnw' 
** testing if installed package can be loaded

install for x64

* installing *source* package 'DECIPHER' ...
** libs
gcc -m64 -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.10-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/RSQLite/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.10-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"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.10-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/RSQLite/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.10-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"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.10-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/RSQLite/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.10-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"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.10-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/RSQLite/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.10-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"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.10-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/RSQLite/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.10-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"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.10-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/RSQLite/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.10-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"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.10-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/RSQLite/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.10-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"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.10-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/RSQLite/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.10-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"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.10-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/RSQLite/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.10-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"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.10-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/RSQLite/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.10-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 -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 R_init_decipher.o ReplaceChars.o -fopenmp -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LE:/biocbld/BBS-2~1.10-/R/bin/x64 -lR
installing to E:/biocbld/bbs-2.10-bioc/meat/DECIPHER.buildbin-libdir/DECIPHER/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DECIPHER' as DECIPHER_1.2.0.zip

* DONE (DECIPHER)