edgeR 3.2.3
Mark Robinson , Davis McCarthy , Yunshun Chen , Gordon Smyth
| 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/edgeR | | Last Changed Rev: 75740 / Revision: 76155 | | Last Changed Date: 2013-04-17 01:55:00 -0700 (Wed, 17 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=edgeR.buildbin-libdir edgeR_3.2.3.tar.gz'
>>>>>>>
* installing *source* package 'edgeR' ...
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./core -I. -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c R_exact_test_by_deviance.cpp -o R_exact_test_by_deviance.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./core -I. -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c R_loess_by_col.cpp -o R_loess_by_col.o
R_loess_by_col.cpp:28:88: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
for (int i=0; i<ncols; ++i) { y_ptrs.push_back(i==0 ? NUMERIC_POINTER(y) : y_ptrs[i-1]+total); }
˜˜˜˜˜˜ ˜^˜
R_loess_by_col.cpp:36:108: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
for (int i=0; i<ncols; ++i) { f_ptrs.push_back(i==0 ? NUMERIC_POINTER(VECTOR_ELT(output, 0)) : f_ptrs[i-1]+total); }
˜˜˜˜˜˜ ˜^˜
R_loess_by_col.cpp:99:47: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
for (int i=0; i<ncols; ++i) { f_ptrs[i][cur_p]=0; }
˜˜˜˜˜˜ ^
R_loess_by_col.cpp:120:51: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
for (int i=0; i<ncols; ++i) { f_ptrs[i][cur_p]+=weight*y_ptrs[i][m]; }
˜˜˜˜˜˜ ^
R_loess_by_col.cpp:120:76: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
for (int i=0; i<ncols; ++i) { f_ptrs[i][cur_p]+=weight*y_ptrs[i][m]; }
˜˜˜˜˜˜ ^
R_loess_by_col.cpp:126:47: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
for (int i=0; i<ncols; ++i) { f_ptrs[i][cur_p]/=total_weight; }
˜˜˜˜˜˜ ^
6 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./core -I. -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c R_cr_adjust.cpp -o R_cr_adjust.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./core -I. -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c R_levenberg.cpp -o R_levenberg.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./core -I. -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c R_maximize_interpolant.cpp -o R_maximize_interpolant.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./core -I. -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c R_one_group.cpp -o R_one_group.o
R_one_group.cpp:24:27: warning: implicit conversion changes signedness: 'const int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
ydptr=(double*) R_alloc(num_libs, sizeof(double));
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./core -I. -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c R_simple_good_turing.cpp -o R_simple_good_turing.o
R_simple_good_turing.cpp:25:35: warning: implicit conversion changes signedness: 'const int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
double* log_obs=(double*)R_alloc(rows, sizeof(double));
˜˜˜˜˜˜˜ ^˜˜˜
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./core -I. -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c core/adj_coxreid.cpp -o core/adj_coxreid.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./core -I. -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c core/glm_levenberg.cpp -o core/glm_levenberg.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./core -I. -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c core/glm_one_group.cpp -o core/glm_one_group.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./core -I. -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c core/interpolator.cpp -o core/interpolator.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I./core -I. -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c core/fmm_spline.c -o core/fmm_spline.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 edgeR.so R_exact_test_by_deviance.o R_loess_by_col.o R_cr_adjust.o R_levenberg.o R_maximize_interpolant.o R_one_group.o R_simple_good_turing.o core/adj_coxreid.o core/glm_levenberg.o core/glm_one_group.o core/interpolator.o core/fmm_spline.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3/x86_64 -L/usr/local/lib/x86_64 -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3 -lgfortran -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/edgeR.buildbin-libdir/edgeR/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (edgeR)
>>>>>>>
>>>>>>> FIXING LINKS FOR edgeR.buildbin-libdir/edgeR/libs//edgeR.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" "edgeR.buildbin-libdir/edgeR/libs//edgeR.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libgfortran.2.dylib" "edgeR.buildbin-libdir/edgeR/libs//edgeR.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" "edgeR.buildbin-libdir/edgeR/libs//edgeR.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libreadline.dylib" "edgeR.buildbin-libdir/edgeR/libs//edgeR.so"