Package: flowType

Version: 2.21.1

Command: rm -rf flowType.buildbin-libdir && mkdir flowType.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh flowType_2.21.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R flowType.buildbin-libdir

StartedAt: 2019-04-09 05:20:58 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 05:22:21 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 82.6 seconds

RetCode: 0

Status:  OK

PackageFile: flowType_2.21.1.tgz

PackageFileSize: 1.239 MiB

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf flowType.buildbin-libdir && mkdir flowType.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh flowType_2.21.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R flowType.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=flowType.buildbin-libdir flowType_2.21.1.tar.gz'
>>>>>>> 

* installing *source* package ‘flowType’ ...
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c countsAndMeans.cpp -o countsAndMeans.o
countsAndMeans.cpp:73:7: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
        for (register int i = 0; i < marker_count; i++)
             ^˜˜˜˜˜˜˜˜
countsAndMeans.cpp:86:7: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
        for (register int i = 0; i < data_count; i++)
             ^˜˜˜˜˜˜˜˜
2 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c flowType.cpp -o flowType.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -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 flowType.so countsAndMeans.o flowType.o numberGenerator.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.9-bioc/meat/flowType.buildbin-libdir/flowType/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
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
* DONE (flowType)


>>>>>>> 
>>>>>>> FIXING LINKS FOR flowType.buildbin-libdir/flowType/libs//flowType.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" "flowType.buildbin-libdir/flowType/libs//flowType.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libgfortran.3.dylib" "flowType.buildbin-libdir/flowType/libs//flowType.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" "flowType.buildbin-libdir/flowType/libs//flowType.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libreadline.dylib" "flowType.buildbin-libdir/flowType/libs//flowType.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libquadmath.0.dylib" "flowType.buildbin-libdir/flowType/libs//flowType.so"