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Package 295/671HostnameOS / ArchBUILDCHECKBUILD BIN
GraphAlignment 1.24.0
Joern P. Meier
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/GraphAlignment
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: GraphAlignment
Version: 1.24.0
Command: rm -rf GraphAlignment.buildbin-libdir && mkdir GraphAlignment.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh GraphAlignment_1.24.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R GraphAlignment.buildbin-libdir
StartedAt: 2013-05-01 12:29:39 -0700 (Wed, 01 May 2013)
EndedAt: 2013-05-01 12:29:42 -0700 (Wed, 01 May 2013)
EllapsedTime: 3.9 seconds
RetCode: 0
Status:  OK 
PackageFile: GraphAlignment_1.24.0.tgz
PackageFileSize: 450.6 KiB

Command output

>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=GraphAlignment.buildbin-libdir GraphAlignment_1.24.0.tar.gz'
>>>>>>> 

* installing *source* package 'GraphAlignment' ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c GA_alloc.c -o GA_alloc.o
GA_alloc.c:57:5: warning: void function 'GA_free' should not return void expression [-Wpedantic]
    return GA_FREE_FUNC(memLoc);
    ^      ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
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 GA_matrix.c -o GA_matrix.o
GA_matrix.c:50:36: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    matrix->elts = (int**)GA_alloc(rows, sizeof(int*));
                          ˜˜˜˜˜˜˜˜ ^˜˜˜
GA_matrix.c:61:42: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        matrix->elts[i] = (int*)GA_alloc(cols, sizeof(int));
                                ˜˜˜˜˜˜˜˜ ^˜˜˜
GA_matrix.c:211:39: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    matrix->elts = (double**)GA_alloc(rows, sizeof(double*));
                             ˜˜˜˜˜˜˜˜ ^˜˜˜
GA_matrix.c:222:45: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        matrix->elts[i] = (double*)GA_alloc(cols, sizeof(double));
                                   ˜˜˜˜˜˜˜˜ ^˜˜˜
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 GA_matrix_R.c -o GA_matrix_R.o
GA_matrix_R.c:39:27: warning: implicit conversion changes signedness: 'int' to 'SEXPTYPE' (aka 'unsigned int') [-Wsign-conversion]
    SEXPTYPE matrixType = TYPEOF(robj);
             ˜˜˜˜˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜
GA_matrix_R.c:94:27: warning: implicit conversion changes signedness: 'int' to 'SEXPTYPE' (aka 'unsigned int') [-Wsign-conversion]
    SEXPTYPE matrixType = TYPEOF(robj);
             ˜˜˜˜˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜
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 GA_message.c -o GA_message.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c GA_vector.c -o GA_vector.o
GA_vector.c:49:32: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    vec->elts = (int*)GA_alloc(size, sizeof(int));
                      ˜˜˜˜˜˜˜˜ ^˜˜˜
GA_vector.c:157:35: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    vec->elts = (double*)GA_alloc(size, sizeof(double));
                         ˜˜˜˜˜˜˜˜ ^˜˜˜
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 GA_vector_R.c -o GA_vector_R.o
GA_vector_R.c:39:24: warning: implicit conversion changes signedness: 'int' to 'SEXPTYPE' (aka 'unsigned int') [-Wsign-conversion]
    SEXPTYPE vecType = TYPEOF(robj);
             ˜˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜
GA_vector_R.c:82:24: warning: implicit conversion changes signedness: 'int' to 'SEXPTYPE' (aka 'unsigned int') [-Wsign-conversion]
    SEXPTYPE vecType = TYPEOF(robj);
             ˜˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜
GA_vector_R.c:125:24: warning: implicit conversion changes signedness: 'int' to 'SEXPTYPE' (aka 'unsigned int') [-Wsign-conversion]
    SEXPTYPE objType = TYPEOF(robj);
             ˜˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜
GA_vector_R.c:139:9: warning: unused variable 'size' [-Wunused-variable]
    int size = LENGTH(robj);
        ^
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 GraphAlignment.c -o GraphAlignment.o
GraphAlignment.c:143:23: warning: add explicit braces to avoid dangling else [-Wdangling-else]
                    } else
                      ^
GraphAlignment.c:164:23: warning: add explicit braces to avoid dangling else [-Wdangling-else]
                    } else
                      ^
GraphAlignment.c:250:24: warning: implicit conversion changes signedness: 'int' to 'SEXPTYPE' (aka 'unsigned int') [-Wsign-conversion]
    SEXPTYPE objType = TYPEOF(robj);
             ˜˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜
GraphAlignment.c:264:9: warning: unused variable 'size' [-Wunused-variable]
    int size = LENGTH(robj);
        ^
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 lap.c -o lap.o
lap.c:67:26: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
  rfree = (row*)GA_alloc(dim, sizeof(row));
                ˜˜˜˜˜˜˜˜ ^˜˜
lap.c:68:28: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
  collist = (col*)GA_alloc(dim, sizeof(col));
                  ˜˜˜˜˜˜˜˜ ^˜˜
lap.c:69:28: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
  matches = (col*)GA_alloc(dim, sizeof(col));
                  ˜˜˜˜˜˜˜˜ ^˜˜
lap.c:70:23: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
  d = (cost*)GA_alloc(dim, sizeof(cost));
             ˜˜˜˜˜˜˜˜ ^˜˜
lap.c:71:25: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
  pred = (row*)GA_alloc(dim, sizeof(row));
               ˜˜˜˜˜˜˜˜ ^˜˜
lap.c:339:32: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
  matched = (boolean*)GA_alloc(dim, sizeof(boolean));
                      ˜˜˜˜˜˜˜˜ ^˜˜
6 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 GraphAlignment.so GA_alloc.o GA_matrix.o GA_matrix_R.o GA_message.o GA_vector.o GA_vector_R.o GraphAlignment.o lap.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/GraphAlignment.buildbin-libdir/GraphAlignment/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (GraphAlignment)


>>>>>>> 
>>>>>>> FIXING LINKS FOR GraphAlignment.buildbin-libdir/GraphAlignment/libs//GraphAlignment.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" "GraphAlignment.buildbin-libdir/GraphAlignment/libs//GraphAlignment.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libgfortran.2.dylib" "GraphAlignment.buildbin-libdir/GraphAlignment/libs//GraphAlignment.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" "GraphAlignment.buildbin-libdir/GraphAlignment/libs//GraphAlignment.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libreadline.dylib" "GraphAlignment.buildbin-libdir/GraphAlignment/libs//GraphAlignment.so"