Package: OUTRIDER

Version: 1.1.4

Command: rm -rf OUTRIDER.buildbin-libdir && mkdir OUTRIDER.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh OUTRIDER_1.1.4.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R OUTRIDER.buildbin-libdir

StartedAt: 2019-04-09 07:29:20 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 07:30:50 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 90.3 seconds

RetCode: 0

Status:  OK

PackageFile: OUTRIDER_1.1.4.tgz

PackageFileSize: 2.215 MiB

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### Running command:
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###   rm -rf OUTRIDER.buildbin-libdir && mkdir OUTRIDER.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh OUTRIDER_1.1.4.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R OUTRIDER.buildbin-libdir
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=OUTRIDER.buildbin-libdir OUTRIDER_1.1.4.tar.gz'
>>>>>>> 

* installing *source* package ‘OUTRIDER’ ...
** using staged installation
** 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/RcppArmadillo/include" -I/usr/local/include -fopenmp  -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.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/RcppArmadillo/include" -I/usr/local/include -fopenmp  -fPIC  -Wall -g -O2  -c loss_n_gradient_functions.cpp -o loss_n_gradient_functions.o
loss_n_gradient_functions.cpp:41:19: warning: unused variable 'c' [-Wunused-variable]
    double b, ll, c;
                  ^
loss_n_gradient_functions.cpp:68:15: warning: unused variable 'c' [-Wunused-variable]
    double b, c;
              ^
2 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 OUTRIDER.so RcppExports.o loss_n_gradient_functions.o -fopenmp -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.9-bioc/meat/OUTRIDER.buildbin-libdir/00LOCK-OUTRIDER/00new/OUTRIDER/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 (OUTRIDER)


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