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BUILD BIN report for Vega on merida2

This page was generated on 2018-10-17 08:48:58 -0400 (Wed, 17 Oct 2018).

Package 1535/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Vega 1.28.0
Sandro Morganella
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/Vega
Branch: RELEASE_3_7
Last Commit: 1fd439c
Last Changed Date: 2018-04-30 10:35:15 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: Vega
Version: 1.28.0
Command: rm -rf Vega.buildbin-libdir && mkdir Vega.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Vega_1.28.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R Vega.buildbin-libdir
StartedAt: 2018-10-17 02:19:06 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 02:20:03 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 56.9 seconds
RetCode: 0
Status:  OK 
PackageFile: Vega_1.28.0.tgz
PackageFileSize: 652.5 KiB

Command output

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###
### Running command:
###
###   rm -rf Vega.buildbin-libdir && mkdir Vega.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Vega_1.28.0.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_1.28.0.tar.gz'
>>>>>>> 

* installing *source* package ‘Vega’ ...
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -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: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:348:68: warning: unused variable 'tmp_lambda2' [-Wunused-variable]
        double lambda, lambda_gradient, stop_lambda_gradient, tmp_lambda, tmp_lambda2;
                                                                          ^
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-3.7-bioc/meat/Vega.buildbin-libdir/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
* 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/3.5/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/3.5/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/3.5/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/3.5/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/3.5/Resources/lib/libquadmath.0.dylib" "Vega.buildbin-libdir/Vega/libs//Vega.so"