Package: RchyOptimyx

Version: 2.23.0

Command: rm -rf RchyOptimyx.buildbin-libdir && mkdir RchyOptimyx.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh RchyOptimyx_2.23.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R RchyOptimyx.buildbin-libdir

StartedAt: 2019-04-09 07:37:14 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 07:37:52 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 38.5 seconds

RetCode: 0

Status:  OK

PackageFile: RchyOptimyx_2.23.0.tgz

PackageFileSize: 750 KiB

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### Running command:
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###   rm -rf RchyOptimyx.buildbin-libdir && mkdir RchyOptimyx.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh RchyOptimyx_2.23.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R RchyOptimyx.buildbin-libdir
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=RchyOptimyx.buildbin-libdir RchyOptimyx_2.23.0.tar.gz'
>>>>>>> 

* installing *source* package ‘RchyOptimyx’ ...
** using staged installation
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -fPIC  -Wall -g -O2  -c RchyOptimyx.cpp -o RchyOptimyx.o
In file included from RchyOptimyx.cpp:13:
./graehl/graph.h:75:8: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  pred = pred;                  // dummy statement to avoid warnings
  ˜˜˜˜ ^ ˜˜˜˜
In file included from RchyOptimyx.cpp:13:
In file included from ./graehl/graph.h:279:
./graehl/kbest.h:37:9: warning: explicitly assigning value of variable of type 'size_t' (aka 'unsigned long') to itself [-Wself-assign]
                dummy = dummy;
                ˜˜˜˜˜ ^ ˜˜˜˜˜
2 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -fPIC  -Wall -g -O2  -c dataRead.cpp -o dataRead.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -fPIC  -Wall -g -O2  -c mystring.cpp -o mystring.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -fPIC  -Wall -g -O2  -c numberGenerator.cpp -o numberGenerator.o
clang++ -std=gnu++11 -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 RchyOptimyx.so RchyOptimyx.o dataRead.o mystring.o numberGenerator.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.9-bioc/meat/RchyOptimyx.buildbin-libdir/00LOCK-RchyOptimyx/00new/RchyOptimyx/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
Creating a new generic function for ‘merge’ in package ‘RchyOptimyx’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
** testing if installed package keeps a record of temporary installation path
* DONE (RchyOptimyx)


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

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libgcc_s.1.dylib" "RchyOptimyx.buildbin-libdir/RchyOptimyx/libs//RchyOptimyx.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libgfortran.3.dylib" "RchyOptimyx.buildbin-libdir/RchyOptimyx/libs//RchyOptimyx.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libreadline.5.2.dylib" "RchyOptimyx.buildbin-libdir/RchyOptimyx/libs//RchyOptimyx.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libreadline.dylib" "RchyOptimyx.buildbin-libdir/RchyOptimyx/libs//RchyOptimyx.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libquadmath.0.dylib" "RchyOptimyx.buildbin-libdir/RchyOptimyx/libs//RchyOptimyx.so"