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BioC 2.12: BUILD BIN report for rtracklayer on petty

This page was generated on 2013-10-09 09:39:41 -0700 (Wed, 09 Oct 2013).

Package 576/671HostnameOS / ArchBUILDCHECKBUILD BIN
rtracklayer 1.20.4
Michael Lawrence
Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/rtracklayer
Last Changed Rev: 78365 / Revision: 81334
Last Changed Date: 2013-07-12 05:44:34 -0700 (Fri, 12 Jul 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  WARNINGS 
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  WARNINGS [ OK ]

Summary

Package: rtracklayer
Version: 1.20.4
Command: rm -rf rtracklayer.buildbin-libdir && mkdir rtracklayer.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh rtracklayer_1.20.4.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R rtracklayer.buildbin-libdir
StartedAt: 2013-10-09 01:04:34 -0700 (Wed, 09 Oct 2013)
EndedAt: 2013-10-09 01:05:13 -0700 (Wed, 09 Oct 2013)
EllapsedTime: 39.1 seconds
RetCode: 0
Status:  OK 
PackageFile: rtracklayer_1.20.4.tgz
PackageFileSize: 1.775 MiB

Command output

>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=rtracklayer.buildbin-libdir rtracklayer_1.20.4.tar.gz'
>>>>>>> 

* installing *source* package 'rtracklayer' ...
** libs
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include"  -g -fPIC  -mtune=core2 -g -O2  -c IRanges_stubs.c -o IRanges_stubs.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include"  -g -fPIC  -mtune=core2 -g -O2  -c R_init_rtracklayer.c -o R_init_rtracklayer.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include"  -g -fPIC  -mtune=core2 -g -O2  -c bigWig.c -o bigWig.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include"  -g -fPIC  -mtune=core2 -g -O2  -c chain_io.c -o chain_io.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include"  -g -fPIC  -mtune=core2 -g -O2  -c twoBit.c -o twoBit.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include"  -g -fPIC  -mtune=core2 -g -O2  -c handlers.c -o handlers.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include"  -g -fPIC  -mtune=core2 -g -O2  -c utils.c -o utils.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include"  -g -fPIC  -mtune=core2 -g -O2  -c ucsc/bPlusTree.c -o ucsc/bPlusTree.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include"  -g -fPIC  -mtune=core2 -g -O2  -c ucsc/bbiRead.c -o ucsc/bbiRead.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include"  -g -fPIC  -mtune=core2 -g -O2  -c ucsc/bbiWrite.c -o ucsc/bbiWrite.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include"  -g -fPIC  -mtune=core2 -g -O2  -c ucsc/bwgCreate.c -o ucsc/bwgCreate.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include"  -g -fPIC  -mtune=core2 -g -O2  -c ucsc/bwgQuery.c -o ucsc/bwgQuery.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include"  -g -fPIC  -mtune=core2 -g -O2  -c ucsc/cirTree.c -o ucsc/cirTree.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include"  -g -fPIC  -mtune=core2 -g -O2  -c ucsc/common.c -o ucsc/common.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include"  -g -fPIC  -mtune=core2 -g -O2  -c ucsc/dnaseq.c -o ucsc/dnaseq.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include"  -g -fPIC  -mtune=core2 -g -O2  -c ucsc/dnautil.c -o ucsc/dnautil.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include"  -g -fPIC  -mtune=core2 -g -O2  -c ucsc/errabort.c -o ucsc/errabort.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include"  -g -fPIC  -mtune=core2 -g -O2  -c ucsc/hash.c -o ucsc/hash.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include"  -g -fPIC  -mtune=core2 -g -O2  -c ucsc/linefile.c -o ucsc/linefile.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include"  -g -fPIC  -mtune=core2 -g -O2  -c ucsc/localmem.c -o ucsc/localmem.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include"  -g -fPIC  -mtune=core2 -g -O2  -c ucsc/sqlNum.c -o ucsc/sqlNum.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include"  -g -fPIC  -mtune=core2 -g -O2  -c ucsc/zlibFace.c -o ucsc/zlibFace.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include"  -g -fPIC  -mtune=core2 -g -O2  -c ucsc/dystring.c -o ucsc/dystring.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include"  -g -fPIC  -mtune=core2 -g -O2  -c ucsc/hmmstats.c -o ucsc/hmmstats.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include"  -g -fPIC  -mtune=core2 -g -O2  -c ucsc/obscure.c -o ucsc/obscure.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include"  -g -fPIC  -mtune=core2 -g -O2  -c ucsc/pipeline.c -o ucsc/pipeline.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include"  -g -fPIC  -mtune=core2 -g -O2  -c ucsc/rangeTree.c -o ucsc/rangeTree.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include"  -g -fPIC  -mtune=core2 -g -O2  -c ucsc/rbTree.c -o ucsc/rbTree.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include"  -g -fPIC  -mtune=core2 -g -O2  -c ucsc/memalloc.c -o ucsc/memalloc.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include"  -g -fPIC  -mtune=core2 -g -O2  -c ucsc/dlist.c -o ucsc/dlist.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include"  -g -fPIC  -mtune=core2 -g -O2  -c ucsc/udc.c -o ucsc/udc.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include"  -g -fPIC  -mtune=core2 -g -O2  -c ucsc/net.c -o ucsc/net.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include"  -g -fPIC  -mtune=core2 -g -O2  -c ucsc/bits.c -o ucsc/bits.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include"  -g -fPIC  -mtune=core2 -g -O2  -c ucsc/twoBit.c -o ucsc/twoBit.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include"  -g -fPIC  -mtune=core2 -g -O2  -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include"  -g -fPIC  -mtune=core2 -g -O2  -c ucsc/internet.c -o ucsc/internet.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include"  -g -fPIC  -mtune=core2 -g -O2  -c ucsc/https.c -o ucsc/https.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include"  -g -fPIC  -mtune=core2 -g -O2  -c ucsc/base64.c -o ucsc/base64.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include"  -g -fPIC  -mtune=core2 -g -O2  -c ucsc/verbose.c -o ucsc/verbose.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include"  -g -fPIC  -mtune=core2 -g -O2  -c ucsc/os.c -o ucsc/os.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include"  -g -fPIC  -mtune=core2 -g -O2  -c ucsc/wildcmp.c -o ucsc/wildcmp.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include"  -g -fPIC  -mtune=core2 -g -O2  -c ucsc/_portimpl.c -o ucsc/_portimpl.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o rtracklayer.so IRanges_stubs.o R_init_rtracklayer.o bigWig.o chain_io.o twoBit.o handlers.o utils.o ucsc/bPlusTree.o ucsc/bbiRead.o ucsc/bbiWrite.o ucsc/bwgCreate.o ucsc/bwgQuery.o ucsc/cirTree.o ucsc/common.o ucsc/dnaseq.o ucsc/dnautil.o ucsc/errabort.o ucsc/hash.o ucsc/linefile.o ucsc/localmem.o ucsc/sqlNum.o ucsc/zlibFace.o ucsc/dystring.o ucsc/hmmstats.o ucsc/obscure.o ucsc/pipeline.o ucsc/rangeTree.o ucsc/rbTree.o ucsc/memalloc.o ucsc/dlist.o ucsc/udc.o ucsc/net.o ucsc/bits.o ucsc/twoBit.o ucsc/_cheapcgi.o ucsc/internet.o ucsc/https.o ucsc/base64.o ucsc/verbose.o ucsc/os.o ucsc/wildcmp.o ucsc/_portimpl.o -lz -pthread -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/rtracklayer.buildbin-libdir/rtracklayer/libs
** R
** data
** demo
** inst
** preparing package for lazy loading
Creating a generic function for 'offset' from package 'stats' in package 'rtracklayer'
Creating a generic function from function 'uri' in package 'rtracklayer'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (rtracklayer)


>>>>>>> 
>>>>>>> FIXING LINKS FOR rtracklayer.buildbin-libdir/rtracklayer/libs//rtracklayer.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" "rtracklayer.buildbin-libdir/rtracklayer/libs//rtracklayer.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libgfortran.2.dylib" "rtracklayer.buildbin-libdir/rtracklayer/libs//rtracklayer.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" "rtracklayer.buildbin-libdir/rtracklayer/libs//rtracklayer.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libreadline.dylib" "rtracklayer.buildbin-libdir/rtracklayer/libs//rtracklayer.so"