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Package 129/514HostnameOS / ArchBUILDCHECKBUILD BIN
DECIPHER 1.0.0
Erik Wright
Snapshot Date: 2012-03-23 18:21:46 -0700 (Fri, 23 Mar 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_9/madman/Rpacks/DECIPHER
Last Changed Rev: 59920 / Revision: 64395
Last Changed Date: 2011-10-31 15:59:03 -0700 (Mon, 31 Oct 2011)
wilson2 Linux (openSUSE 11.4) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK [ OK ]
pitt Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: DECIPHER
Version: 1.0.0
Command: rm -rf DECIPHER.buildbin-libdir && mkdir DECIPHER.buildbin-libdir && D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=DECIPHER.buildbin-libdir DECIPHER_1.0.0.tar.gz
StartedAt: 2012-03-24 03:38:44 -0700 (Sat, 24 Mar 2012)
EndedAt: 2012-03-24 03:39:41 -0700 (Sat, 24 Mar 2012)
EllapsedTime: 57.0 seconds
RetCode: 0
Status:  OK  
PackageFile: DECIPHER_1.0.0.zip
PackageFileSize: 728.8 KiB

Command output


install for i386

* installing *source* package 'DECIPHER' ...
** libs
gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/RSQLite/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/stats/include"      -O3 -Wall  -std=gnu99 -mtune=core2 -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/RSQLite/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/stats/include"      -O3 -Wall  -std=gnu99 -mtune=core2 -c ClusterML.c -o ClusterML.o
gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/RSQLite/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/stats/include"      -O3 -Wall  -std=gnu99 -mtune=core2 -c ClusterNJ.c -o ClusterNJ.o
ClusterNJ.c: In function 'clusterNJ':
ClusterNJ.c:263:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
ClusterNJ.c:273:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
ClusterNJ.c:433:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
ClusterNJ.c:445:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
ClusterNJ.c:192:62: warning: 'minC' may be used uninitialized in this function [-Wuninitialized]
ClusterNJ.c:192:56: warning: 'minR' may be used uninitialized in this function [-Wuninitialized]
gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/RSQLite/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/stats/include"      -O3 -Wall  -std=gnu99 -mtune=core2 -c ClusterUPGMA.c -o ClusterUPGMA.o
ClusterUPGMA.c: In function 'clusterUPGMA':
ClusterUPGMA.c:180:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
ClusterUPGMA.c:190:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
ClusterUPGMA.c:340:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
ClusterUPGMA.c:352:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
ClusterUPGMA.c:121:62: warning: 'minC' may be used uninitialized in this function [-Wuninitialized]
ClusterUPGMA.c:121:56: warning: 'minR' may be used uninitialized in this function [-Wuninitialized]
gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/RSQLite/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/stats/include"      -O3 -Wall  -std=gnu99 -mtune=core2 -c CommonGaps.c -o CommonGaps.o
gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/RSQLite/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/stats/include"      -O3 -Wall  -std=gnu99 -mtune=core2 -c ConsensusSequence.c -o ConsensusSequence.o
gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/RSQLite/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/stats/include"      -O3 -Wall  -std=gnu99 -mtune=core2 -c DistanceMatrix.c -o DistanceMatrix.o
DistanceMatrix.c: In function 'distMatrix':
DistanceMatrix.c:171:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/RSQLite/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/stats/include"      -O3 -Wall  -std=gnu99 -mtune=core2 -c R_init_decipher.c -o R_init_decipher.o
gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/RSQLite/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/stats/include"      -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 ClusterML.o ClusterNJ.o ClusterUPGMA.o CommonGaps.o ConsensusSequence.o DistanceMatrix.o R_init_decipher.o ReplaceChars.o -LD:/biocbld/BBS-2˜1.9-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-2.9-bioc/meat/DECIPHER.buildbin-libdir/DECIPHER/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'DECIPHERing.Rnw' 
   'FindChimeras.Rnw' 
** testing if installed package can be loaded

add DLL for x64

* installing *source* package 'DECIPHER' ...
** libs
gcc -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/RSQLite/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/stats/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/RSQLite/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/stats/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c ClusterML.c -o ClusterML.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/RSQLite/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/stats/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c ClusterNJ.c -o ClusterNJ.o
ClusterNJ.c: In function 'clusterNJ':
ClusterNJ.c:263:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
ClusterNJ.c:273:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
ClusterNJ.c:433:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
ClusterNJ.c:445:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
ClusterNJ.c:192:41: warning: 'minCol' may be used uninitialized in this function [-Wuninitialized]
ClusterNJ.c:192:33: warning: 'minRow' may be used uninitialized in this function [-Wuninitialized]
gcc -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/RSQLite/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/stats/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c ClusterUPGMA.c -o ClusterUPGMA.o
ClusterUPGMA.c: In function 'clusterUPGMA':
ClusterUPGMA.c:180:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
ClusterUPGMA.c:190:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
ClusterUPGMA.c:340:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
ClusterUPGMA.c:352:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
ClusterUPGMA.c:121:41: warning: 'minCol' may be used uninitialized in this function [-Wuninitialized]
ClusterUPGMA.c:121:33: warning: 'minRow' may be used uninitialized in this function [-Wuninitialized]
gcc -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/RSQLite/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/stats/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c CommonGaps.c -o CommonGaps.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/RSQLite/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/stats/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c ConsensusSequence.c -o ConsensusSequence.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/RSQLite/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/stats/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c DistanceMatrix.c -o DistanceMatrix.o
DistanceMatrix.c: In function 'distMatrix':
DistanceMatrix.c:171:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
gcc -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/RSQLite/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/stats/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c R_init_decipher.c -o R_init_decipher.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/RSQLite/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/stats/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -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 ClusterML.o ClusterNJ.o ClusterUPGMA.o CommonGaps.o ConsensusSequence.o DistanceMatrix.o R_init_decipher.o ReplaceChars.o -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LD:/biocbld/BBS-2˜1.9-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-2.9-bioc/meat/DECIPHER.buildbin-libdir/DECIPHER/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DECIPHER' as DECIPHER_1.0.0.zip

* DONE (DECIPHER)