IRanges 2.0.1
Bioconductor Package Maintainer
| Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/IRanges | | Last Changed Rev: 97568 / Revision: 102249 | | Last Changed Date: 2014-12-11 11:40:54 -0800 (Thu, 11 Dec 2014) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | OK | WARNINGS | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | WARNINGS | OK |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | WARNINGS | [ OK ] |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | WARNINGS | OK |
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### Running command:
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### rm -rf IRanges.buildbin-libdir && mkdir IRanges.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh IRanges_2.0.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R IRanges.buildbin-libdir
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>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=IRanges.buildbin-libdir IRanges_2.0.1.tar.gz'
>>>>>>>
* installing *source* package ‘IRanges’ ...
** libs
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include" -fPIC -mtune=core2 -g -O2 -Wall -c CompressedIRangesList_class.c -o CompressedIRangesList_class.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include" -fPIC -mtune=core2 -g -O2 -Wall -c CompressedList_class.c -o CompressedList_class.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include" -fPIC -mtune=core2 -g -O2 -Wall -c DataFrame_class.c -o DataFrame_class.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include" -fPIC -mtune=core2 -g -O2 -Wall -c GappedRanges_class.c -o GappedRanges_class.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include" -fPIC -mtune=core2 -g -O2 -Wall -c Grouping_class.c -o Grouping_class.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include" -fPIC -mtune=core2 -g -O2 -Wall -c IRanges_class.c -o IRanges_class.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include" -fPIC -mtune=core2 -g -O2 -Wall -c IRanges_constructor.c -o IRanges_constructor.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include" -fPIC -mtune=core2 -g -O2 -Wall -c IntervalTree.c -o IntervalTree.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include" -fPIC -mtune=core2 -g -O2 -Wall -c NCList.c -o NCList.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include" -fPIC -mtune=core2 -g -O2 -Wall -c R_init_IRanges.c -o R_init_IRanges.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include" -fPIC -mtune=core2 -g -O2 -Wall -c RangedData_class.c -o RangedData_class.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include" -fPIC -mtune=core2 -g -O2 -Wall -c Ranges_class.c -o Ranges_class.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include" -fPIC -mtune=core2 -g -O2 -Wall -c Ranges_comparison.c -o Ranges_comparison.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include" -fPIC -mtune=core2 -g -O2 -Wall -c RleViews_utils.c -o RleViews_utils.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include" -fPIC -mtune=core2 -g -O2 -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include" -fPIC -mtune=core2 -g -O2 -Wall -c SimpleRangesList_class.c -o SimpleRangesList_class.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include" -fPIC -mtune=core2 -g -O2 -Wall -c common.c -o common.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include" -fPIC -mtune=core2 -g -O2 -Wall -c coverage_methods.c -o coverage_methods.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include" -fPIC -mtune=core2 -g -O2 -Wall -c dlist.c -o dlist.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include" -fPIC -mtune=core2 -g -O2 -Wall -c errabort.c -o errabort.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include" -fPIC -mtune=core2 -g -O2 -Wall -c inter_range_methods.c -o inter_range_methods.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include" -fPIC -mtune=core2 -g -O2 -Wall -c localmem.c -o localmem.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include" -fPIC -mtune=core2 -g -O2 -Wall -c memalloc.c -o memalloc.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include" -fPIC -mtune=core2 -g -O2 -Wall -c rbTree.c -o rbTree.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include" -fPIC -mtune=core2 -g -O2 -Wall -c ucsc_handlers.c -o ucsc_handlers.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/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -L/usr/local/lib -o IRanges.so CompressedIRangesList_class.o CompressedList_class.o DataFrame_class.o GappedRanges_class.o Grouping_class.o IRanges_class.o IRanges_constructor.o IntervalTree.o NCList.o R_init_IRanges.o RangedData_class.o Ranges_class.o Ranges_comparison.o RleViews_utils.o S4Vectors_stubs.o SimpleRangesList_class.o common.o coverage_methods.o dlist.o errabort.o inter_range_methods.o localmem.o memalloc.o rbTree.o ucsc_handlers.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.0-bioc/meat/IRanges.buildbin-libdir/IRanges/libs
** R
** inst
** preparing package for lazy loading
Warning: undefined slot classes in definition of "RangesNSBS": subscript(class "Ranges")
in method for ‘NSBS’ with signature ‘"Ranges"’: no definition for class “Ranges”
in method for ‘extractROWS’ with signature ‘"vectorORfactor","Ranges"’: no definition for class “Ranges”
in method for ‘extractROWS’ with signature ‘"matrix","Ranges"’: no definition for class “Ranges”
Creating a generic function for ‘head’ from package ‘utils’ in package ‘IRanges’
Creating a generic function for ‘tail’ from package ‘utils’ in package ‘IRanges’
Creating a generic function for ‘window’ from package ‘stats’ in package ‘IRanges’
Creating a generic function for ‘window<-’ from package ‘stats’ in package ‘IRanges’
Creating a generic function for ‘rev’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘with’ from package ‘base’ in package ‘IRanges’
in method for ‘coerce’ with signature ‘"Hits","IntegerList"’: no definition for class “IntegerList”
Creating a generic function for ‘stack’ from package ‘utils’ in package ‘IRanges’
in method for ‘!’ with signature ‘"CompressedList"’: no definition for class “CompressedList”
in method for ‘match’ with signature ‘"CompressedList","list"’: no definition for class “CompressedList”
in method for ‘match’ with signature ‘"CompressedList","vector"’: no definition for class “CompressedList”
in method for ‘duplicated’ with signature ‘"CompressedList"’: no definition for class “CompressedList”
in method for ‘unique’ with signature ‘"CompressedList"’: no definition for class “CompressedList”
in method for ‘is.na’ with signature ‘"CompressedList"’: no definition for class “CompressedList”
Creating a generic function for ‘mean’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘which.max’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘which.min’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘split’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘split<-’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘drop’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘which’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘diff’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘var’ from package ‘stats’ in package ‘IRanges’
Creating a generic function for ‘cov’ from package ‘stats’ in package ‘IRanges’
Creating a generic function for ‘cor’ from package ‘stats’ in package ‘IRanges’
Creating a generic function for ‘sd’ from package ‘stats’ in package ‘IRanges’
Creating a generic function for ‘median’ from package ‘stats’ in package ‘IRanges’
Creating a generic function for ‘quantile’ from package ‘stats’ in package ‘IRanges’
Creating a generic function for ‘mad’ from package ‘stats’ in package ‘IRanges’
Creating a generic function for ‘IQR’ from package ‘stats’ in package ‘IRanges’
Creating a generic function for ‘smoothEnds’ from package ‘stats’ in package ‘IRanges’
Creating a generic function for ‘runmed’ from package ‘stats’ in package ‘IRanges’
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘chartr’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘tolower’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘toupper’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘sub’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘gsub’ from package ‘base’ in package ‘IRanges’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (IRanges)
>>>>>>>
>>>>>>> FIXING LINKS FOR IRanges.buildbin-libdir/IRanges/libs//IRanges.so
>>>>>>>
install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.1/Resources/lib/libgcc_s.1.dylib" "IRanges.buildbin-libdir/IRanges/libs//IRanges.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/3.1/Resources/lib/libgfortran.2.dylib" "IRanges.buildbin-libdir/IRanges/libs//IRanges.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.1/Resources/lib/libreadline.5.2.dylib" "IRanges.buildbin-libdir/IRanges/libs//IRanges.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.1/Resources/lib/libreadline.dylib" "IRanges.buildbin-libdir/IRanges/libs//IRanges.so"