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BioC 3.6: BUILD BIN report for motifmatchr on veracruz1

This page was generated on 2017-08-16 13:50:34 -0400 (Wed, 16 Aug 2017).

Package 861/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
motifmatchr 0.99.8
Alicia Schep
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/motifmatchr
Last Changed Rev: 130141 / Revision: 131943
Last Changed Date: 2017-06-06 11:29:38 -0400 (Tue, 06 Jun 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: motifmatchr
Version: 0.99.8
Command: rm -rf motifmatchr.buildbin-libdir && mkdir motifmatchr.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh motifmatchr_0.99.8.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R motifmatchr.buildbin-libdir
StartedAt: 2017-08-16 10:53:28 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 10:54:44 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 76.2 seconds
RetCode: 0
Status:  OK 
PackageFile: motifmatchr_0.99.8.tgz
PackageFileSize: 178.8 KiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf motifmatchr.buildbin-libdir && mkdir motifmatchr.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh motifmatchr_0.99.8.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R motifmatchr.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=motifmatchr.buildbin-libdir motifmatchr_0.99.8.tar.gz'
>>>>>>> 

* installing *source* package ‘motifmatchr’ ...
** libs
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I./MOODS/ -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I./MOODS/ -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c r_interface.cpp -o r_interface.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I./MOODS/ -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c MOODS/scanner.cpp -o MOODS/scanner.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I./MOODS/ -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c MOODS/motif_h.cpp -o MOODS/motif_h.o
MOODS/motif_h.cpp:256:25: warning: '&' within '^' [-Wbitwise-op-parentheses]
            CODE = MASK & (CODE << SHIFT) ^ alphabet_map[s[ii + i + q - 1]];
                   ˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜
MOODS/motif_h.cpp:256:25: note: place parentheses around the '&' expression to silence this warning
            CODE = MASK & (CODE << SHIFT) ^ alphabet_map[s[ii + i + q - 1]];
                        ^
                   (                     )
1 warning generated.
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I./MOODS/ -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c MOODS/motif_0.cpp -o MOODS/motif_0.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I./MOODS/ -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c MOODS/moods_tools.cpp -o MOODS/moods_tools.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I./MOODS/ -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c MOODS/moods_scan.cpp -o MOODS/moods_scan.o
MOODS/moods_scan.cpp:97:14: warning: unused variable 'done' [-Wunused-variable]
        bool done = 0;
             ^
MOODS/moods_scan.cpp:252:33: warning: '&' within '|' [-Wbitwise-op-parentheses]
                    CODE = MASK & (CODE << SHIFT) | alphabet_map[seq[i+j+q-1]];
                           ˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ˜
MOODS/moods_scan.cpp:252:33: note: place parentheses around the '&' expression to silence this warning
                    CODE = MASK & (CODE << SHIFT) | alphabet_map[seq[i+j+q-1]];
                                ^
                           (                     )
2 warnings generated.
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I./MOODS/ -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c MOODS/moods_parsers.cpp -o MOODS/moods_parsers.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I./MOODS/ -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c MOODS/moods_misc.cpp -o MOODS/moods_misc.o
clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I./MOODS/ -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c MOODS/match_types.cpp -o MOODS/match_types.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I. -I./MOODS/ -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppArmadillo/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c motifmatchr_init.c -o motifmatchr_init.o
clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o motifmatchr.so ./RcppExports.o ./r_interface.o ./MOODS/scanner.o ./MOODS/motif_h.o ./MOODS/motif_0.o ./MOODS/moods_tools.o ./MOODS/moods_scan.o ./MOODS/moods_parsers.o ./MOODS/moods_misc.o ./MOODS/match_types.o ./motifmatchr_init.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.6-bioc/meat/motifmatchr.buildbin-libdir/motifmatchr/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (motifmatchr)


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

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libgcc_s.1.dylib" "motifmatchr.buildbin-libdir/motifmatchr/libs//motifmatchr.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libgfortran.3.dylib" "motifmatchr.buildbin-libdir/motifmatchr/libs//motifmatchr.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libreadline.5.2.dylib" "motifmatchr.buildbin-libdir/motifmatchr/libs//motifmatchr.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libreadline.dylib" "motifmatchr.buildbin-libdir/motifmatchr/libs//motifmatchr.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libquadmath.0.dylib" "motifmatchr.buildbin-libdir/motifmatchr/libs//motifmatchr.so"