BioC 3.4: BUILD BIN report for bgx on morelia

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### Running command:
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###   rm -rf bgx.buildbin-libdir && mkdir bgx.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh bgx_1.40.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R bgx.buildbin-libdir
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=bgx.buildbin-libdir bgx_1.40.0.tar.gz'
>>>>>>> 

* installing *source* package ‘bgx’ ...
checking for gcc... clang
checking for C compiler default output file name... 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 C compiler vendor... gnu
checking whether C compiler accepts -ffast-math... yes
checking whether C compiler accepts -O3... yes
checking build system type... i386-apple-darwin13.4.0
checking host system type... i386-apple-darwin13.4.0
checking for gcc architecture flag... 
checking for x86 cpuid 0 output... d:756e6547:6c65746e:49656e69
checking for x86 cpuid 1 output... 306a9:2100800:7fbae3ff:bfebfbff
checking whether C compiler accepts -march=pentium2... no
checking whether C compiler accepts -mcpu=pentium2... yes
checking for gcc architecture flag... -mcpu=pentium2
checking for clang option to accept ISO C99... none needed
checking for main in -lm... yes
Untarring Boost header files...
checking for an ANSI C-conforming const... yes
checking for inline... inline
configure: creating ./config.status
config.status: creating src/Makevars
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I ../boostIncl -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -ffast-math -O3 -DUSING_R -c bgx.cc -o bgx.o
In file included from bgx.cc:29:
./bgx_updates.hh:47:8: warning: private field 'categories' is not used [-Wunused-private-field]
  int* categories;
       ^
./bgx_updates.hh:310:8: warning: private field 'categories' is not used [-Wunused-private-field]
  int *categories;
       ^
./bgx_updates.hh:311:7: warning: private field 'numberCategories' is not used [-Wunused-private-field]
  int numberCategories;
      ^
3 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I ../boostIncl -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -ffast-math -O3 -DUSING_R -c bgx_frontend.cc -o bgx_frontend.o
bgx_frontend.cc:251:16: warning: comparison between NULL and non-pointer ('int' and NULL) [-Wnull-arithmetic]
  if(SampleSets==NULL){
     ˜˜˜˜˜˜˜˜˜˜^ ˜˜˜˜
bgx_frontend.cc:261:15: warning: comparison between NULL and non-pointer ('int' and NULL) [-Wnull-arithmetic]
  if(ProbeSets==NULL){
     ˜˜˜˜˜˜˜˜˜^ ˜˜˜˜
bgx_frontend.cc:271:16: warning: comparison between NULL and non-pointer ('int' and NULL) [-Wnull-arithmetic]
  if(Categories==NULL){
     ˜˜˜˜˜˜˜˜˜˜^ ˜˜˜˜
bgx_frontend.cc:281:22: warning: comparison between NULL and non-pointer ('int' and NULL) [-Wnull-arithmetic]
  if(UnknownProbeSeqs==NULL){
     ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^ ˜˜˜˜
bgx_frontend.cc:291:18: warning: comparison between NULL and non-pointer ('int' and NULL) [-Wnull-arithmetic]
  if(GenesToWatch==NULL){
     ˜˜˜˜˜˜˜˜˜˜˜˜^ ˜˜˜˜
bgx_frontend.cc:301:33: warning: comparison between NULL and non-pointer ('int' and NULL) [-Wnull-arithmetic]
  if(FirstProbeInEachGeneToWatch==NULL){
     ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^ ˜˜˜˜
bgx_frontend.cc:311:8: warning: comparison between NULL and non-pointer ('int' and NULL) [-Wnull-arithmetic]
  if(PM==NULL){
     ˜˜^ ˜˜˜˜
bgx_frontend.cc:316:8: warning: comparison between NULL and non-pointer ('int' and NULL) [-Wnull-arithmetic]
  if(MM==NULL){
     ˜˜^ ˜˜˜˜
8 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I ../boostIncl -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -g -O2 -mcpu=pentium2  -ffast-math -O3 -c qnorm.c -o qnorm.o
clang: warning: argument unused during compilation: '-mcpu=pentium2'
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I ../boostIncl -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -ffast-math -O3 -DUSING_R -c rundir.cc -o rundir.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I ../boostIncl -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -ffast-math -O3 -DUSING_R -c sokal.cc -o sokal.o
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 bgx.so bgx.o bgx_frontend.o qnorm.o rundir.o sokal.o -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
rm -r ../boostIncl
installing to /Users/biocbuild/bbs-3.4-bioc/meat/bgx.buildbin-libdir/bgx/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 (bgx)


>>>>>>> 
>>>>>>> FIXING LINKS FOR bgx.buildbin-libdir/bgx/libs//bgx.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" "bgx.buildbin-libdir/bgx/libs//bgx.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.3/Resources/lib/libgfortran.3.dylib" "bgx.buildbin-libdir/bgx/libs//bgx.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" "bgx.buildbin-libdir/bgx/libs//bgx.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.3/Resources/lib/libreadline.dylib" "bgx.buildbin-libdir/bgx/libs//bgx.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.3/Resources/lib/libquadmath.0.dylib" "bgx.buildbin-libdir/bgx/libs//bgx.so"
BioC 3.4: BUILD BIN report for bgx on morelia

Summary

Command output
