flipflop 1.2.2
Elsa Bernard
| Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/flipflop | | Last Changed Rev: 94109 / Revision: 95116 | | Last Changed Date: 2014-09-13 23:29:35 -0700 (Sat, 13 Sep 2014) |
| zin2 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | NotNeeded | OK | WARNINGS | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | WARNINGS | OK |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | WARNINGS | OK |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | WARNINGS | [ OK ] |
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### Running command:
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### rm -rf flipflop.buildbin-libdir && mkdir flipflop.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh flipflop_1.2.2.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R flipflop.buildbin-libdir
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>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=flipflop.buildbin-libdir flipflop_1.2.2.tar.gz'
>>>>>>>
* installing *source* package ‘flipflop’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c R_init_flipflop.c -o R_init_flipflop.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -stdlib=libstdc++ -DUSE_BLAS_LIB -DNDEBUG -O3 -mtune=native -Wall -fPIC -Wall -mtune=core2 -g -O2 -c align.cpp -o align.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -stdlib=libstdc++ -DUSE_BLAS_LIB -DNDEBUG -O3 -mtune=native -Wall -fPIC -Wall -mtune=core2 -g -O2 -c auxiliaryio.cpp -o auxiliaryio.o
auxiliaryio.cpp:157:1: warning: control may reach end of non-void function [-Wreturn-type]
}
^
auxiliaryio.cpp:892:9: warning: unused variable 'id' [-Wunused-variable]
int id;
^
2 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -stdlib=libstdc++ -DUSE_BLAS_LIB -DNDEBUG -O3 -mtune=native -Wall -fPIC -Wall -mtune=core2 -g -O2 -c bed2sam.cpp -o bed2sam.o
bed2sam.cpp:149:9: warning: unused variable 'xs' [-Wunused-variable]
char xs;
^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -stdlib=libstdc++ -DUSE_BLAS_LIB -DNDEBUG -O3 -mtune=native -Wall -fPIC -Wall -mtune=core2 -g -O2 -c bedio.cpp -o bedio.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -stdlib=libstdc++ -DUSE_BLAS_LIB -DNDEBUG -O3 -mtune=native -Wall -fPIC -Wall -mtune=core2 -g -O2 -c common.cpp -o common.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -stdlib=libstdc++ -DUSE_BLAS_LIB -DNDEBUG -O3 -mtune=native -Wall -fPIC -Wall -mtune=core2 -g -O2 -c cvganalysis.cpp -o cvganalysis.o
cvganalysis.cpp:156:12: warning: unused variable 'prevjump' [-Wunused-variable]
bool prevjump=false;
^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -stdlib=libstdc++ -DUSE_BLAS_LIB -DNDEBUG -O3 -mtune=native -Wall -fPIC -Wall -mtune=core2 -g -O2 -c ffProcesssam.cpp -o ffProcesssam.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -stdlib=libstdc++ -DUSE_BLAS_LIB -DNDEBUG -O3 -mtune=native -Wall -fPIC -Wall -mtune=core2 -g -O2 -c instanceio.cpp -o instanceio.o
instanceio.cpp:125:9: warning: unused variable 'currenttypeorder' [-Wunused-variable]
int currenttypeorder=-1;
^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -stdlib=libstdc++ -DUSE_BLAS_LIB -DNDEBUG -O3 -mtune=native -Wall -fPIC -Wall -mtune=core2 -g -O2 -c parseopt.cpp -o parseopt.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -stdlib=libstdc++ -DUSE_BLAS_LIB -DNDEBUG -O3 -mtune=native -Wall -fPIC -Wall -mtune=core2 -g -O2 -c rangeset.cpp -o rangeset.o
rangeset.cpp:331:8: warning: unused variable 't' [-Wunused-variable]
long t=0;
^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -stdlib=libstdc++ -DUSE_BLAS_LIB -DNDEBUG -O3 -mtune=native -Wall -fPIC -Wall -mtune=core2 -g -O2 -c readgroup.cpp -o readgroup.o
readgroup.cpp:1098:14: warning: unused variable 'nneg' [-Wunused-variable]
int npos=0,nneg=0;
^
readgroup.cpp:1098:7: warning: unused variable 'npos' [-Wunused-variable]
int npos=0,nneg=0;
^
readgroup.cpp:1097:7: warning: unused variable 'r' [-Wunused-variable]
int r=0;
^
3 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -stdlib=libstdc++ -DUSE_BLAS_LIB -DNDEBUG -O3 -mtune=native -Wall -fPIC -Wall -mtune=core2 -g -O2 -c samio.cpp -o samio.o
samio.cpp:98:11: warning: unused variable 'dp2' [-Wunused-variable]
range_t dp2=dp;
^
samio.cpp:106:7: warning: unused variable 'currentreadlen' [-Wunused-variable]
int currentreadlen=0;
^
samio.cpp:102:7: warning: unused variable 'rangecounter' [-Wunused-variable]
int rangecounter=1;
^
3 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -stdlib=libstdc++ -DUSE_BLAS_LIB -DNDEBUG -O3 -mtune=native -Wall -fPIC -Wall -mtune=core2 -g -O2 -c spams.cpp -o spams.o
spams.cpp:2515:14: warning: explicitly assigning a variable of type 'void *' to itself [-Wself-assign]
clientdata = clientdata;
˜˜˜˜˜˜˜˜˜˜ ^ ˜˜˜˜˜˜˜˜˜˜
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I. -Ispams/linalg -Ispams/prox -Ispams/decomp -Ispams/dags -stdlib=libstdc++ -DUSE_BLAS_LIB -DNDEBUG -O3 -mtune=native -Wall -fPIC -Wall -mtune=core2 -g -O2 -c structdef.cpp -o structdef.o
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o flipflop.so R_init_flipflop.o align.o auxiliaryio.o bed2sam.o bedio.o common.o cvganalysis.o ffProcesssam.o instanceio.o parseopt.o rangeset.o readgroup.o samio.o spams.o structdef.o -lstdc++ -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -lcblas -stdlib=libstdc++ -L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2 -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.14-bioc/meat/flipflop.buildbin-libdir/flipflop/libs
** R
** inst
** preparing package for lazy loading
Warning: class "numLike" is defined (with package slot ‘Matrix’) but no metadata object found to revise subclass information---not exported? Making a copy in package ‘flipflop’
Creating a generic function for ‘print’ from package ‘base’ in package ‘flipflop’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (flipflop)
>>>>>>>
>>>>>>> FIXING LINKS FOR flipflop.buildbin-libdir/flipflop/libs//flipflop.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" "flipflop.buildbin-libdir/flipflop/libs//flipflop.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.1/Resources/lib/libgfortran.3.dylib" "flipflop.buildbin-libdir/flipflop/libs//flipflop.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" "flipflop.buildbin-libdir/flipflop/libs//flipflop.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.1/Resources/lib/libreadline.dylib" "flipflop.buildbin-libdir/flipflop/libs//flipflop.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.1/Resources/lib/libquadmath.0.dylib" "flipflop.buildbin-libdir/flipflop/libs//flipflop.so"