GenomicRanges 1.12.2
Bioconductor Package Maintainer
| 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/GenomicRanges | | Last Changed Rev: 75712 / Revision: 76155 | | Last Changed Date: 2013-04-16 14:58:27 -0700 (Tue, 16 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 ] |
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=GenomicRanges.buildbin-libdir GenomicRanges_1.12.2.tar.gz'
>>>>>>>
* installing *source* package 'GenomicRanges' ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c IRanges_stubs.c -o IRanges_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/IRanges/include" -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c R_init_GenomicRanges.c -o R_init_GenomicRanges.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c cigar_utils.c -o cigar_utils.o
cigar_utils.c:682:26: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memset(INTEGER(ans), 0, LENGTH(ans) * sizeof(int));
^˜˜˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest)) \
^
cigar_utils.c:682:26: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memset(INTEGER(ans), 0, LENGTH(ans) * sizeof(int));
^˜˜˜˜˜˜˜˜˜˜ ˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
: __inline_memset_chk (dest, val, len))
^
cigar_utils.c:680:18: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
allOPs_length = strlen(allOPs);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜
cigar_utils.c:1092:27: warning: implicit conversion changes signedness: 'int' to 'Rboolean' [-Wsign-conversion]
Rboolean _narrow_left = asLogical(narrow_left);
˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:946:20: note: expanded from macro 'asLogical'
#define asLogical Rf_asLogical
^
cigar_utils.c:1171:27: warning: implicit conversion changes signedness: 'int' to 'Rboolean' [-Wsign-conversion]
Rboolean _narrow_left = asLogical(narrow_left);
˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:946:20: note: expanded from macro 'asLogical'
#define asLogical Rf_asLogical
^
5 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/IRanges/include" -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c transcript_utils.c -o transcript_utils.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o GenomicRanges.so IRanges_stubs.o R_init_GenomicRanges.o cigar_utils.o transcript_utils.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/GenomicRanges.buildbin-libdir/GenomicRanges/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (GenomicRanges)
>>>>>>>
>>>>>>> FIXING LINKS FOR GenomicRanges.buildbin-libdir/GenomicRanges/libs//GenomicRanges.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" "GenomicRanges.buildbin-libdir/GenomicRanges/libs//GenomicRanges.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libgfortran.2.dylib" "GenomicRanges.buildbin-libdir/GenomicRanges/libs//GenomicRanges.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" "GenomicRanges.buildbin-libdir/GenomicRanges/libs//GenomicRanges.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libreadline.dylib" "GenomicRanges.buildbin-libdir/GenomicRanges/libs//GenomicRanges.so"