Package: Vega

Version: 1.34.0

Command: rm -rf Vega.buildbin-libdir && mkdir Vega.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Vega_1.34.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R Vega.buildbin-libdir

StartedAt: 2020-04-15 09:04:04 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 09:04:50 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 45.7 seconds

RetCode: 0

Status:  OK

PackageFile: Vega_1.34.0.tgz

PackageFileSize: 654.4 KiB

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### Running command:
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###   rm -rf Vega.buildbin-libdir && mkdir Vega.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Vega_1.34.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R Vega.buildbin-libdir
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=Vega.buildbin-libdir Vega_1.34.0.tar.gz'
>>>>>>> 

* installing *source* package ‘Vega’ ...
** using staged installation
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c vega.c -o vega.o
vega.c:369:20: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
        lambda_gradient = abs(lambda);
                          ^
vega.c:369:20: note: use function 'fabs' instead
        lambda_gradient = abs(lambda);
                          ^~~
                          fabs
vega.c:348:68: warning: unused variable 'tmp_lambda2' [-Wunused-variable]
        double lambda, lambda_gradient, stop_lambda_gradient, tmp_lambda, tmp_lambda2;
                                                                          ^
vega.c:355:13: warning: unused variable 'maxptr' [-Wunused-variable]
        node max, *maxptr, tmp_node;
                   ^
vega.c:347:6: warning: unused variable 'index' [-Wunused-variable]
        int index;
            ^
vega.c:560:64: warning: unused variable 'next_mean' [-Wunused-variable]
        double lambda, first_term, second_term, prev_mean, curr_mean, next_mean;
                                                                      ^
5 warnings generated.
clang -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 Vega.so vega.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.10-bioc/meat/Vega.buildbin-libdir/00LOCK-Vega/00new/Vega/libs
** R
** data
** 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 (Vega)


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