affy 1.38.1
Rafael A. Irizarry
| 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/affy | | Last Changed Rev: 75788 / Revision: 76155 | | Last Changed Date: 2013-04-18 14:30:32 -0700 (Thu, 18 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=affy.buildbin-libdir affy_1.38.1.tar.gz'
>>>>>>>
* installing *source* package 'affy' ...
creating cache ./config.cache
checking how to run the C preprocessor... cc -E
checking for main in -lz... yes
checking for zlib.h... yes
checking if zlib version >= 1.1.3... yes
updating cache ./config.cache
creating ./config.status
creating src/Makevars
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DHAVE_ZLIB=1 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/preprocessCore/include" -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c chipbackground.c -o chipbackground.o
chipbackground.c:379:29: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
qsort(data_by_sector[j],cur_n[j],sizeof(double),(int(*)(const void*, const void*))sort_double);
˜˜˜˜˜ ^˜˜˜˜˜˜˜
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DHAVE_ZLIB=1 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/preprocessCore/include" -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c getall_locations.c -o getall_locations.o
getall_locations.c:38:31: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
nbElements = (int *)R_alloc(nb_affyid, sizeof(int));
˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DHAVE_ZLIB=1 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/preprocessCore/include" -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c mas5calls.c -o mas5calls.o
mas5calls.c:96:31: warning: implicit conversion turns floating-point number into integer: 'double' to 'size_t' (aka 'unsigned long') [-Wconversion]
r = (double *) R_alloc(nx,sizeof(double));
˜˜˜˜˜˜˜ ^˜
mas5calls.c:97:31: warning: implicit conversion turns floating-point number into integer: 'double' to 'size_t' (aka 'unsigned long') [-Wconversion]
absx = (double *) R_alloc(nx,sizeof(double));
˜˜˜˜˜˜˜ ^˜
mas5calls.c:98:28: warning: implicit conversion turns floating-point number into integer: 'double' to 'size_t' (aka 'unsigned long') [-Wconversion]
xidx = (int *) R_alloc(nx,sizeof(int));
˜˜˜˜˜˜˜ ^˜
mas5calls.c:104:30: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
rsort_with_index(absx,xidx,nx);
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜
mas5calls.c:105:13: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
rank(absx,nx,r);
˜˜˜˜ ^˜
mas5calls.c:151:30: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
ignore = (int *) R_alloc(n, sizeof(int));
˜˜˜˜˜˜˜ ^
mas5calls.c:175:27: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
dv = (double *) R_alloc(n, sizeof(double));
˜˜˜˜˜˜˜ ^
7 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DHAVE_ZLIB=1 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/preprocessCore/include" -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c rma2.c -o rma2.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DHAVE_ZLIB=1 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/preprocessCore/include" -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c rma_common.c -o rma_common.o
rma_common.c:64:19: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memcpy(buffer,x,length*sizeof(double));
^˜˜˜˜˜˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest)) \
^
rma_common.c:64:19: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memcpy(buffer,x,length*sizeof(double));
^˜˜˜˜˜˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
: __inline_memcpy_chk (dest, src, len))
^
rma_common.c:106:19: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memcpy(buffer,x,length*sizeof(double));
^˜˜˜˜˜˜
/usr/include/secure/_string.h:52:41: note: expanded from macro 'memcpy'
? __builtin___memcpy_chk (dest, src, len, __darwin_obsz0 (dest)) \
^
rma_common.c:106:19: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
memcpy(buffer,x,length*sizeof(double));
^˜˜˜˜˜˜
/usr/include/secure/_string.h:53:38: note: expanded from macro 'memcpy'
: __inline_memcpy_chk (dest, src, len))
^
4 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 affy.so chipbackground.o getall_locations.o mas5calls.o rma2.o rma_common.o -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/affy.buildbin-libdir/affy/libs
** R
** data
** demo
** inst
** preparing package for lazy loading
Creating a generic function for 'open' from package 'base' in package 'affy'
Creating a generic function for 'close' from package 'base' in package 'affy'
Creating a generic function for 'barplot' from package 'graphics' in package 'affy'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (affy)
>>>>>>>
>>>>>>> FIXING LINKS FOR affy.buildbin-libdir/affy/libs//affy.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" "affy.buildbin-libdir/affy/libs//affy.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libgfortran.2.dylib" "affy.buildbin-libdir/affy/libs//affy.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" "affy.buildbin-libdir/affy/libs//affy.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libreadline.dylib" "affy.buildbin-libdir/affy/libs//affy.so"