Back to the "Multiple platform build/check report" A  B  C [D] E  F  G  H  I  J  K  L  M  N  O  P  Q  R  S  T  U  V  W  X  Y  Z 

BioC 3.2: BUILD BIN report for DiffBind on oaxaca

This page was generated on 2016-04-23 10:25:28 -0700 (Sat, 23 Apr 2016).

Package 274/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DiffBind 1.16.3
Rory Stark
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/DiffBind
Last Changed Rev: 112064 / Revision: 116712
Last Changed Date: 2015-12-31 06:21:50 -0800 (Thu, 31 Dec 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: DiffBind
Version: 1.16.3
Command: rm -rf DiffBind.buildbin-libdir && mkdir DiffBind.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh DiffBind_1.16.3.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R DiffBind.buildbin-libdir
StartedAt: 2016-04-23 05:37:41 -0700 (Sat, 23 Apr 2016)
EndedAt: 2016-04-23 05:38:24 -0700 (Sat, 23 Apr 2016)
EllapsedTime: 42.9 seconds
RetCode: 0
Status:  OK 
PackageFile: DiffBind_1.16.3.tgz
PackageFileSize: 2.088 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf DiffBind.buildbin-libdir && mkdir DiffBind.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh DiffBind_1.16.3.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R DiffBind.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=DiffBind.buildbin-libdir DiffBind_1.16.3.tar.gz'
>>>>>>> 

* installing *source* package ‘DiffBind’ ...
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c bamReader.cpp -o bamReader.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c bedReader.cpp -o bedReader.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c bitBucket.cpp -o bitBucket.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c croi_func.cpp -o croi_func.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c croi_main.cpp -o croi_main.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c densitySet.cpp -o densitySet.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c iBucket.cpp -o iBucket.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c interval.cpp -o interval.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c intervalDensity.cpp -o intervalDensity.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c intervalNode.cpp -o intervalNode.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c intervalSet.cpp -o intervalSet.o
intervalSet.cpp:14:5: warning: delete called on 'bode::IntervalTree' that has virtual functions but non-virtual destructor [-Wdelete-non-virtual-dtor]
    delete it->second;
    ^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c intervalTree.cpp -o intervalTree.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c mergeOne.c -o mergeOne.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c nodeGroup.cpp -o nodeGroup.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c reader.cpp -o reader.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c sequence.cpp -o sequence.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c util.cpp -o util.o
clang++ -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 DiffBind.so bamReader.o bedReader.o bitBucket.o croi_func.o croi_main.o densitySet.o iBucket.o interval.o intervalDensity.o intervalNode.o intervalSet.o intervalTree.o mergeOne.o nodeGroup.o reader.o sequence.o util.o /Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/usrlib//libbam.a /Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/usrlib//libbcf.a /Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rsamtools/usrlib//libtabix.a -lz -pthread -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
clang: warning: argument unused during compilation: '-pthread'
installing to /Users/biocbuild/bbs-3.2-bioc/meat/DiffBind.buildbin-libdir/DiffBind/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 (DiffBind)


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

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.2/Resources/lib/libgcc_s.1.dylib" "DiffBind.buildbin-libdir/DiffBind/libs//DiffBind.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.2/Resources/lib/libgfortran.3.dylib" "DiffBind.buildbin-libdir/DiffBind/libs//DiffBind.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.2/Resources/lib/libreadline.5.2.dylib" "DiffBind.buildbin-libdir/DiffBind/libs//DiffBind.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.2/Resources/lib/libreadline.dylib" "DiffBind.buildbin-libdir/DiffBind/libs//DiffBind.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.2/Resources/lib/libquadmath.0.dylib" "DiffBind.buildbin-libdir/DiffBind/libs//DiffBind.so"