BioC 3.4: BUILD BIN report for MotIV on morelia

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### Running command:
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###   rm -rf MotIV.buildbin-libdir && mkdir MotIV.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh MotIV_1.30.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R MotIV.buildbin-libdir
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=MotIV.buildbin-libdir MotIV_1.30.0.tar.gz'
>>>>>>> 

* installing *source* package ‘MotIV’ ...
checking for gcc... clang
checking for C compiler default output file name... rm: a.out.dSYM: is a directory
a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether clang accepts -g... yes
checking for clang option to accept ISO C89... none needed
checking for gsl-config... /usr/local/bin/gsl-config
checking for GSL - version >= 1.6... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c Alignment.cpp -o Alignment.o
Alignment.cpp:185:9: warning: unused variable 'currTwo' [-Wunused-variable]
        Motif* currTwo = two;
               ^
Alignment.cpp:178:12: warning: unused variable 'aL_B' [-Wunused-variable]
        int aL_A, aL_B; 
                  ^
Alignment.cpp:179:14: warning: unused variable 'for_B' [-Wunused-variable]
        bool for_A, for_B;
                    ^
Alignment.cpp:177:24: warning: unused variable 'i2_B' [-Wunused-variable]
        int i1_A, i2_A, i1_B, i2_B;
                              ^
Alignment.cpp:176:17: warning: unused variable 'score2' [-Wunused-variable]
        double score1, score2, bestScore=0;
                       ^
Alignment.cpp:177:18: warning: unused variable 'i1_B' [-Wunused-variable]
        int i1_A, i2_A, i1_B, i2_B;
                        ^
6 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c ColumnComp.cpp -o ColumnComp.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c DeclareAll.cpp -o DeclareAll.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c Motif.cpp -o Motif.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c MotifDistances.cpp -o MotifDistances.o
MotifDistances.cpp:115:2: warning: delete called on 'ColumnComp' that is abstract but has non-virtual destructor [-Wdelete-non-virtual-dtor]
        delete(CC);
        ^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c MotifMatch.cpp -o MotifMatch.o
MotifMatch.cpp:120:2: warning: delete called on 'ColumnComp' that is abstract but has non-virtual destructor [-Wdelete-non-virtual-dtor]
        delete(CC);
        ^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c PlatformSupport.cpp -o PlatformSupport.o
PlatformSupport.cpp:156:10: warning: explicitly assigning a variable of type 'int' to itself [-Wself-assign]
                currCnt=currCnt;
                ˜˜˜˜˜˜˜^˜˜˜˜˜˜˜
PlatformSupport.cpp:112:11: warning: variable 'input' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
        else if (inputDB!=0)
                 ^˜˜˜˜˜˜˜˜˜
PlatformSupport.cpp:126:22: note: uninitialized use occurs here
        inputName=GET_NAMES(input);
                            ^˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/Rdefines.h:149:36: note: expanded from macro 'GET_NAMES'
#define GET_NAMES(x)            Rf_getAttrib(x, R_NamesSymbol)
                                             ^
PlatformSupport.cpp:112:7: note: remove the 'if' if its condition is always true
        else if (inputDB!=0)
             ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
PlatformSupport.cpp:103:23: note: initialize the variable 'input' to silence this warning
        SEXP inputName, input;
                             ^
                              = NULL
2 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c RandPSSMGen.cpp -o RandPSSMGen.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c generateScoresDB.cpp -o generateScoresDB.o
generateScoresDB.cpp:127:2: warning: delete called on 'ColumnComp' that is abstract but has non-virtual destructor [-Wdelete-non-virtual-dtor]
        delete(CC);
        ^
1 warning generated.
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o MotIV.so Alignment.o ColumnComp.o DeclareAll.o Motif.o MotifDistances.o MotifMatch.o PlatformSupport.o RandPSSMGen.o generateScoresDB.o -lgsl -lgslcblas -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.4-bioc/meat/MotIV.buildbin-libdir/MotIV/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a new generic function for ‘filter’ in package ‘MotIV’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (MotIV)


>>>>>>> 
>>>>>>> FIXING LINKS FOR MotIV.buildbin-libdir/MotIV/libs//MotIV.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.3/Resources/lib/libgcc_s.1.dylib" "MotIV.buildbin-libdir/MotIV/libs//MotIV.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.3/Resources/lib/libgfortran.3.dylib" "MotIV.buildbin-libdir/MotIV/libs//MotIV.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.3/Resources/lib/libreadline.5.2.dylib" "MotIV.buildbin-libdir/MotIV/libs//MotIV.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.3/Resources/lib/libreadline.dylib" "MotIV.buildbin-libdir/MotIV/libs//MotIV.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.3/Resources/lib/libquadmath.0.dylib" "MotIV.buildbin-libdir/MotIV/libs//MotIV.so"
BioC 3.4: BUILD BIN report for MotIV on morelia

Summary

Command output
