Package: slalom

Version: 1.6.0

Command: rm -rf slalom.buildbin-libdir && mkdir slalom.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh slalom_1.6.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R slalom.buildbin-libdir

StartedAt: 2019-10-16 09:26:52 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 09:28:14 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 82.1 seconds

RetCode: 0

Status:  OK

PackageFile: slalom_1.6.0.tgz

PackageFileSize: 19.98 MiB

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### Running command:
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###   rm -rf slalom.buildbin-libdir && mkdir slalom.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh slalom_1.6.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R slalom.buildbin-libdir
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=slalom.buildbin-libdir slalom_1.6.0.tar.gz'
>>>>>>> 

* installing *source* package ‘slalom’ ...
** 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"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -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"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c slalom-classes.cpp -o slalom-classes.o
slalom-classes.cpp:223:20: warning: unused variable 'meanerr' [-Wunused-variable]
            double meanerr = arma::mean(error);
                   ^
slalom-classes.cpp:202:12: warning: unused variable 'meanerr' [-Wunused-variable]
    double meanerr = arma::mean(error);
           ^
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 slalom.so RcppExports.o slalom-classes.o -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/slalom.buildbin-libdir/00LOCK-slalom/00new/slalom/libs
** R
** data
*** moving datasets to lazyload DB
** 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 (slalom)


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