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Package 169/671HostnameOS / ArchBUILDCHECKBUILD BIN
DECIPHER 1.6.0
Erik Wright
Snapshot Date: 2013-04-30 17:01:37 -0700 (Tue, 30 Apr 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/DECIPHER
Last Changed Rev: 75263 / Revision: 76155
Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 
pelham Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK [ OK ]

Summary

Package: DECIPHER
Version: 1.6.0
Command: rm -rf DECIPHER.buildbin-libdir && mkdir DECIPHER.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh DECIPHER_1.6.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R DECIPHER.buildbin-libdir
StartedAt: 2013-05-01 12:18:06 -0700 (Wed, 01 May 2013)
EndedAt: 2013-05-01 12:18:27 -0700 (Wed, 01 May 2013)
EllapsedTime: 21.9 seconds
RetCode: 0
Status:  OK 
PackageFile: DECIPHER_1.6.0.tgz
PackageFileSize: 1.124 MiB

Command output

>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=DECIPHER.buildbin-libdir DECIPHER_1.6.0.tar.gz'
>>>>>>> 

* installing *source* package 'DECIPHER' ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/stats/include"   -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c Biostrings_stubs.c -o Biostrings_stubs.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/stats/include"   -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c CalculateDeltaG.c -o CalculateDeltaG.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/stats/include"   -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c ClusterML.c -o ClusterML.o
ClusterML.c:269:40: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        double *Ls = (double *) R_alloc(length*8, sizeof(double));
                                ˜˜˜˜˜˜˜ ˜˜˜˜˜˜^˜
ClusterML.c:270:32: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        int *widths = (int *) R_alloc(length, sizeof(int));
                              ˜˜˜˜˜˜˜ ^˜˜˜˜˜
2 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/stats/include"   -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c ClusterNJ.c -o ClusterNJ.o
ClusterNJ.c:202:9: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
        size = sqrt(length(x)); // square distance matrix dimension
             ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ClusterNJ.c:207:43: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        double *dMatrix = (double *) R_alloc(size*size, sizeof(double)); // final row & col contain cluster numbers
                                     ˜˜˜˜˜˜˜ ˜˜˜˜^˜˜˜˜
ClusterNJ.c:266:11: warning: unknown pragma ignored [-Wunknown-pragmas]
                #pragma omp parallel for private(i,j,minR,minC,minH) schedule(guided)
                        ^
ClusterNJ.c:276:12: warning: unknown pragma ignored [-Wunknown-pragmas]
                        #pragma omp critical
                                ^
ClusterNJ.c:436:11: warning: unknown pragma ignored [-Wunknown-pragmas]
                #pragma omp parallel for private(i,j) schedule(guided)
                        ^
ClusterNJ.c:448:11: warning: unknown pragma ignored [-Wunknown-pragmas]
                #pragma omp parallel for private(i,j) schedule(guided)
                        ^
ClusterNJ.c:486:24: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
                        *rPercentComplete = floor(100*soFar/total);
                                          ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
7 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/stats/include"   -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c ClusterUPGMA.c -o ClusterUPGMA.o
ClusterUPGMA.c:131:9: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
        size = sqrt(length(x)); // square distance matrix dimension
             ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ClusterUPGMA.c:136:43: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        double *dMatrix = (double *) R_alloc(size*size, sizeof(double)); // final row & col contain cluster numbers
                                     ˜˜˜˜˜˜˜ ˜˜˜˜^˜˜˜˜
ClusterUPGMA.c:183:11: warning: unknown pragma ignored [-Wunknown-pragmas]
                #pragma omp parallel for private(i,j,minR,minC,minH) schedule(guided)
                        ^
ClusterUPGMA.c:193:12: warning: unknown pragma ignored [-Wunknown-pragmas]
                        #pragma omp critical
                                ^
ClusterUPGMA.c:343:11: warning: unknown pragma ignored [-Wunknown-pragmas]
                #pragma omp parallel for private(i,j) schedule(guided)
                        ^
ClusterUPGMA.c:355:11: warning: unknown pragma ignored [-Wunknown-pragmas]
                #pragma omp parallel for private(i,j) schedule(guided)
                        ^
ClusterUPGMA.c:393:24: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
                        *rPercentComplete = floor(100*soFar/total);
                                          ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
7 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/stats/include"   -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c CommonGaps.c -o CommonGaps.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/stats/include"   -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c ConsensusSequence.c -o ConsensusSequence.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/stats/include"   -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c DistanceMatrix.c -o DistanceMatrix.o
DistanceMatrix.c:174:12: warning: unknown pragma ignored [-Wunknown-pragmas]
                        #pragma omp parallel for private(j,x_j,seqLength_j,start,end) schedule(guided)
                                ^
DistanceMatrix.c:213:25: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
                                *rPercentComplete = floor(100*(double)soFar/((x_length - 1)*x_length+(x_length - 1)));
                                                  ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
2 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/stats/include"   -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c MultiMatch.c -o MultiMatch.o
MultiMatch.c:189:10: warning: unknown pragma ignored [-Wunknown-pragmas]
        #pragma omp parallel for private(i, j) schedule(guided)
                ^
MultiMatch.c:215:10: warning: unknown pragma ignored [-Wunknown-pragmas]
        #pragma omp parallel for private(i, j) schedule(guided)
                ^
2 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/stats/include"   -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c R_init_decipher.c -o R_init_decipher.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/stats/include"   -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c ReplaceChars.c -o ReplaceChars.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/stats/include"   -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c TerminalMismatch.c -o TerminalMismatch.o
TerminalMismatch.c:46:10: warning: unknown pragma ignored [-Wunknown-pragmas]
        #pragma omp parallel for private(i,j,lp,lt,l,mm,count,end,gaps,probe,target) schedule(guided)
                ^
1 warning generated.
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o DECIPHER.so 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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/DECIPHER.buildbin-libdir/DECIPHER/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (DECIPHER)


>>>>>>> 
>>>>>>> FIXING LINKS FOR DECIPHER.buildbin-libdir/DECIPHER/libs//DECIPHER.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libgcc_s.1.dylib" "DECIPHER.buildbin-libdir/DECIPHER/libs//DECIPHER.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libgfortran.2.dylib" "DECIPHER.buildbin-libdir/DECIPHER/libs//DECIPHER.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libreadline.5.2.dylib" "DECIPHER.buildbin-libdir/DECIPHER/libs//DECIPHER.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libreadline.dylib" "DECIPHER.buildbin-libdir/DECIPHER/libs//DECIPHER.so"