Biobase 2.20.0
Bioconductor Package Maintainer
| 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/Biobase | | 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=Biobase.buildbin-libdir Biobase_2.20.0.tar.gz'
>>>>>>>
* installing *source* package 'Biobase' ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c Rinit.c -o Rinit.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c anyMissing.c -o anyMissing.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c envir.c -o envir.o
envir.c:21:61: warning: implicit conversion changes signedness: 'int' to 'SEXPTYPE' (aka 'unsigned int') [-Wsign-conversion]
error("arg 'x' must be a 'list', not '%s'", type2char(TYPEOF(x)));
˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
envir.c:42:36: warning: implicit conversion changes signedness: 'int' to 'Rboolean' [-Wsign-conversion]
PROTECT(nms = R_lsInternal(e1, all_nms));
˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:547:31: note: expanded from macro 'PROTECT'
#define PROTECT(s) Rf_protect(s)
^
envir.c:61:23: warning: implicit conversion changes signedness: 'int' to 'SEXPTYPE' (aka 'unsigned int') [-Wsign-conversion]
type2char(TYPEOF(x)));
˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
envir.c:65:23: warning: implicit conversion changes signedness: 'int' to 'SEXPTYPE' (aka 'unsigned int') [-Wsign-conversion]
type2char(TYPEOF(env)));
˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
envir.c:119:32: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
rowData = (double *) R_alloc(ncol, sizeof(double));
˜˜˜˜˜˜˜ ^˜˜˜
envir.c:179:25: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
prefix[i] = toupper(first[i]);
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
envir.c:185:21: warning: implicit conversion loses integer precision: 'int' to 'char' [-Wconversion]
c = toupper(c);
˜ ^˜˜˜˜˜˜˜˜˜
envir.c:162:14: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
min_nc = strlen(CHAR(STRING_ELT(x, 0)));
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
envir.c:167:14: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
nc = strlen(CHAR(ans));
˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
9 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c matchpt.c -o matchpt.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c rowMedians.c -o rowMedians.o
rowMedians.c:31:32: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
rowData = (double *) R_alloc(ncol, sizeof(double));
˜˜˜˜˜˜˜ ^˜˜˜
rowMedians.c:53:31: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
colOffset = (int *) R_alloc(ncol, sizeof(int));
˜˜˜˜˜˜˜ ^˜˜˜
rowMedians.c:158:29: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
rowData = (int *) R_alloc(ncol, sizeof(int));
˜˜˜˜˜˜˜ ^˜˜˜
rowMedians.c:179:31: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
colOffset = (int *) R_alloc(ncol, sizeof(int));
˜˜˜˜˜˜˜ ^˜˜˜
4 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c sublist_extract.c -o sublist_extract.o
sublist_extract.c:28:25: warning: implicit conversion changes signedness: 'int' to 'SEXPTYPE' (aka 'unsigned int') [-Wsign-conversion]
type2char(TYPEOF(v)));
˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜
sublist_extract.c:149:35: warning: implicit conversion changes signedness: 'int' to 'SEXPTYPE' (aka 'unsigned int') [-Wsign-conversion]
PROTECT(ans = allocVector(TYPEOF(el), length(L)));
˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:547:31: note: expanded from macro 'PROTECT'
#define PROTECT(s) Rf_protect(s)
^
sublist_extract.c:171:29: warning: implicit conversion changes signedness: 'int' to 'SEXPTYPE' (aka 'unsigned int') [-Wsign-conversion]
type2char(TYPEOF(el)));
˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
3 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 Biobase.so Rinit.o anyMissing.o envir.o matchpt.o rowMedians.o sublist_extract.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/Biobase.buildbin-libdir/Biobase/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 (Biobase)
>>>>>>>
>>>>>>> FIXING LINKS FOR Biobase.buildbin-libdir/Biobase/libs//Biobase.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" "Biobase.buildbin-libdir/Biobase/libs//Biobase.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libgfortran.2.dylib" "Biobase.buildbin-libdir/Biobase/libs//Biobase.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" "Biobase.buildbin-libdir/Biobase/libs//Biobase.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libreadline.dylib" "Biobase.buildbin-libdir/Biobase/libs//Biobase.so"