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Package 69/671HostnameOS / ArchBUILDCHECKBUILD BIN
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 ]

Summary

Package: Biobase
Version: 2.20.0
Command: rm -rf Biobase.buildbin-libdir && mkdir Biobase.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Biobase_2.20.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R Biobase.buildbin-libdir
StartedAt: 2013-05-01 12:08:43 -0700 (Wed, 01 May 2013)
EndedAt: 2013-05-01 12:09:02 -0700 (Wed, 01 May 2013)
EllapsedTime: 19.1 seconds
RetCode: 0
Status:  OK 
PackageFile: Biobase_2.20.0.tgz
PackageFileSize: 2.242 MiB

Command output

>>>>>>> 
>>>>>>> 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"