plier 1.30.0
Crispin Miller
| 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/plier | | Last Changed Rev: 75263 / Revision: 76155 | | Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 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 |
| pelham | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | WARNINGS | [ OK ] |
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=plier.buildbin-libdir plier_1.30.0.tar.gz'
>>>>>>>
* installing *source* package 'plier' ...
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c affyplier.cpp -o affyplier.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c plier_impl.cpp -o plier_impl.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c plieralg.cpp -o plieralg.o
plieralg.cpp:491:33: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
memset(NewtonCDeriv, 0, pData->m_nAnalyses*sizeof(double));
˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜
plieralg.cpp:492:33: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
memset(NewtonCGrad, 0, pData->m_nAnalyses*sizeof(double));
˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜
plieralg.cpp:493:33: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
memset(NewtonADeriv, 0, pData->m_nProbes*sizeof(double));
˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜
plieralg.cpp:494:32: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
memset(NewtonAGrad, 0, pData->m_nProbes*sizeof(double));
˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜
plieralg.cpp:1164:35: warning: implicit conversion changes signedness: 'long' to 'unsigned long' [-Wsign-conversion]
memset(NewtonAStep, 0, pData->m_nProbes*sizeof(double)); // no change to affinities based on data
˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜
plieralg.cpp:49:12: warning: unused variable 'g_ErrorCode' [-Wunused-variable]
static int g_ErrorCode=NoError;
^
6 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c rwrapper.cpp -o rwrapper.o
rwrapper.cpp:75:31: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
sp->set_sea_attenuation(attenuation);
˜˜ ^˜˜˜˜˜˜˜˜˜˜
rwrapper.cpp:79:30: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
sp->set_plier_gmcutoff(gmcutoff);
˜˜ ^˜˜˜˜˜˜˜
rwrapper.cpp:80:34: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
sp->set_plier_probepenalty(probepenalty);
˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
rwrapper.cpp:81:33: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
sp->set_plier_concpenalty(concpenalty);
˜˜ ^˜˜˜˜˜˜˜˜˜˜
rwrapper.cpp:263:48: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
pms = (double *) R_alloc(MAX_PROBESET_SIZE * *num_exp,sizeof(double));
˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜
rwrapper.cpp:268:48: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
mms = (double *) R_alloc(MAX_PROBESET_SIZE * *num_exp,sizeof(double));
˜˜˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜
rwrapper.cpp:275:34: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
pm_ptr = (double **) R_alloc(*num_exp,sizeof(double *));
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
rwrapper.cpp:280:34: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
mm_ptr = (double **) R_alloc(*num_exp,sizeof(double *));
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
8 warnings generated.
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o plier.so affyplier.o plier_impl.o plieralg.o rwrapper.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/plier.buildbin-libdir/plier/libs
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (plier)
>>>>>>>
>>>>>>> FIXING LINKS FOR plier.buildbin-libdir/plier/libs//plier.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" "plier.buildbin-libdir/plier/libs//plier.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libgfortran.2.dylib" "plier.buildbin-libdir/plier/libs//plier.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" "plier.buildbin-libdir/plier/libs//plier.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libreadline.dylib" "plier.buildbin-libdir/plier/libs//plier.so"