Package: simulatorZ

Version: 1.17.0

Command: rm -rf simulatorZ.buildbin-libdir && mkdir simulatorZ.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh simulatorZ_1.17.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R simulatorZ.buildbin-libdir

StartedAt: 2019-04-09 07:47:39 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 07:48:14 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 34.8 seconds

RetCode: 0

Status:  OK

PackageFile: simulatorZ_1.17.0.tgz

PackageFileSize: 304.5 KiB

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf simulatorZ.buildbin-libdir && mkdir simulatorZ.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh simulatorZ_1.17.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R simulatorZ.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=simulatorZ.buildbin-libdir simulatorZ_1.17.0.tar.gz'
>>>>>>> 

* installing *source* package ‘simulatorZ’ ...
** 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 coxformatrices.cpp -o coxformatrices.o
coxformatrices.cpp:79:17: warning: suggest braces around initialization of subobject [-Wmissing-braces]
                NULL
                ^˜˜˜
                {   }
/usr/local/clang4/bin/../lib/clang/4.0.0/include/stddef.h:100:18: note: expanded from macro 'NULL'
#    define NULL __null
                 ^˜˜˜˜˜
coxformatrices.cpp:529:6: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
     register int i,j;
     ^˜˜˜˜˜˜˜˜
coxformatrices.cpp:529:6: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
     register int i,j;
     ^˜˜˜˜˜˜˜˜
coxformatrices.cpp:530:6: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
     register double temp;
     ^˜˜˜˜˜˜˜˜
coxformatrices.cpp:570:6: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
     register double temp;
     ^˜˜˜˜˜˜˜˜
coxformatrices.cpp:571:6: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
     register int i,j,k;
     ^˜˜˜˜˜˜˜˜
coxformatrices.cpp:571:6: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
     register int i,j,k;
     ^˜˜˜˜˜˜˜˜
coxformatrices.cpp:571:6: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
     register int i,j,k;
     ^˜˜˜˜˜˜˜˜
coxformatrices.cpp:657:5: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
    register int i;
    ^˜˜˜˜˜˜˜˜
coxformatrices.cpp:658:5: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
    register double **pointer;
    ^˜˜˜˜˜˜˜˜
10 warnings generated.
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 simulatorZ.so coxformatrices.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.9-bioc/meat/simulatorZ.buildbin-libdir/00LOCK-simulatorZ/00new/simulatorZ/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (simulatorZ)


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