Package: simpleaffy

Version: 2.59.0

Command: rm -rf simpleaffy.buildbin-libdir && mkdir simpleaffy.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh simpleaffy_2.59.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R simpleaffy.buildbin-libdir

StartedAt: 2019-04-09 07:47:36 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 07:48:05 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 28.7 seconds

RetCode: 0

Status:  OK

PackageFile: simpleaffy_2.59.0.tgz

PackageFileSize: 736.5 KiB

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### Running command:
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###   rm -rf simpleaffy.buildbin-libdir && mkdir simpleaffy.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh simpleaffy_2.59.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R simpleaffy.buildbin-libdir
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=simpleaffy.buildbin-libdir simpleaffy_2.59.0.tar.gz'
>>>>>>> 

* installing *source* package ‘simpleaffy’ ...
** using staged installation
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -fPIC  -Wall -g -O2  -c simpleaffy.c -o simpleaffy.o
simpleaffy.c:440:30: warning: incompatible pointer types passing 'FILE *' (aka 'struct __sFILE *') to parameter of type 'const char *' [-Wincompatible-pointer-types]
    if(gn >= ngrid) REprintf(stderr,"Really ouch! %d %d\n",gn,ends[gn]);
                             ^˜˜˜˜˜
/usr/include/stdio.h:218:16: note: expanded from macro 'stderr'
#define stderr  __stderrp
                ^˜˜˜˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/R_ext/Print.h:43:27: note: passing argument to parameter here
void REprintf(const char *, ...);
                          ^
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 simpleaffy.so simpleaffy.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.9-bioc/meat/simpleaffy.buildbin-libdir/00LOCK-simpleaffy/00new/simpleaffy/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 (simpleaffy)


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