Package: sva

Version: 3.31.1

Command: rm -rf sva.buildbin-libdir && mkdir sva.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh sva_3.31.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R sva.buildbin-libdir

StartedAt: 2019-04-09 07:51:17 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 07:52:05 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 47.7 seconds

RetCode: 0

Status:  OK

PackageFile: sva_3.31.1.tgz

PackageFileSize: 483.6 KiB

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### Running command:
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###   rm -rf sva.buildbin-libdir && mkdir sva.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh sva_3.31.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R sva.buildbin-libdir
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=sva.buildbin-libdir sva_3.31.1.tar.gz'
>>>>>>> 

* installing *source* package ‘sva’ ...
** using staged installation
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -fPIC  -Wall -g -O2  -c sva.c -o sva.o
sva.c:29:3: warning: suggest braces around initialization of subobject [-Wmissing-braces]
  NULL
  ^˜˜˜
  {   }
/usr/local/clang4/bin/../lib/clang/4.0.0/include/stddef.h:105:16: note: expanded from macro 'NULL'
#  define NULL ((void*)0)
               ^˜˜˜˜˜˜˜˜˜
1 warning 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 sva.so sva.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.9-bioc/meat/sva.buildbin-libdir/00LOCK-sva/00new/sva/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 (sva)


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