sigPathway 1.28.0
Weil Lai
| 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/sigPathway | | 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 | 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=sigPathway.buildbin-libdir sigPathway_1.28.0.tar.gz'
>>>>>>>
* installing *source* package 'sigPathway' ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c calc_gene_set_internal.c -o calc_gene_set_internal.o
calc_gene_set_internal.c:318:35: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
R_qsort(tsn_null_abs_sorted, 1, len_tsn_null);
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c calc_gene_set_stat.c -o calc_gene_set_stat.o
calc_gene_set_stat.c:118:34: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
if( memcmp(pperm, phenotype, *ncol*sizeof(double)) != 0 ) {
^˜˜˜˜˜
calc_gene_set_stat.c:223:25: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
if( memcmp(tpV, tV, *n_ps*sizeof(double)) != 0 ) {
^˜˜˜˜˜
calc_gene_set_stat.c:342:34: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
if( memcmp(pperm, phenotype, *ncol*sizeof(double)) != 0 ) {
^˜˜˜˜˜
3 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c calc_probe_stat.c -o calc_probe_stat.o
calc_probe_stat.c:53:36: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
if( memcmp(pperm, phenotype, *ncol*sizeof(double)) != 0 ) {
^˜˜˜˜˜
calc_probe_stat.c:229:25: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memset(Yig_mean, 0, *ngroups*sizeof(double));
^˜˜˜˜˜˜˜˜
/usr/include/secure/_string.h:74:41: note: expanded from macro 'memset'
? __builtin___memset_chk (dest, val, len, __darwin_obsz0 (dest)) \
^
calc_probe_stat.c:229:25: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memset(Yig_mean, 0, *ngroups*sizeof(double));
^˜˜˜˜˜˜˜˜
/usr/include/secure/_string.h:75:38: note: expanded from macro 'memset'
: __inline_memset_chk (dest, val, len))
^
3 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c calc_weights.c -o calc_weights.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c matrix_fn.c -o matrix_fn.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c permute.c -o permute.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c shuffle.c -o shuffle.o
shuffle.c:26:11: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
j = i + (int)(*m-i)*unif_rand();
˜ ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
shuffle.c:46:11: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
j = i + (int)(*m-i)*unif_rand();
˜ ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
2 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c sigPathway.c -o sigPathway.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 sigPathway.so calc_gene_set_internal.o calc_gene_set_stat.o calc_probe_stat.o calc_weights.o matrix_fn.o permute.o shuffle.o sigPathway.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/sigPathway.buildbin-libdir/sigPathway/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 (sigPathway)
>>>>>>>
>>>>>>> FIXING LINKS FOR sigPathway.buildbin-libdir/sigPathway/libs//sigPathway.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" "sigPathway.buildbin-libdir/sigPathway/libs//sigPathway.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libgfortran.2.dylib" "sigPathway.buildbin-libdir/sigPathway/libs//sigPathway.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" "sigPathway.buildbin-libdir/sigPathway/libs//sigPathway.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libreadline.dylib" "sigPathway.buildbin-libdir/sigPathway/libs//sigPathway.so"