Package: limma

Version: 3.16.2

Command: rm -rf limma.buildbin-libdir && mkdir limma.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh limma_3.16.2.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R limma.buildbin-libdir

StartedAt: 2013-05-01 12:35:01 -0700 (Wed, 01 May 2013)

EndedAt: 2013-05-01 12:35:10 -0700 (Wed, 01 May 2013)

EllapsedTime: 9.3 seconds

RetCode: 0

Status:  OK

PackageFile: limma_3.16.2.tgz

PackageFileSize: 1.49 MiB

>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=limma.buildbin-libdir limma_3.16.2.tar.gz'
>>>>>>> 

* installing *source* package 'limma' ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c normexp.c -o normexp.o
normexp.c:153:20: warning: magnitude of floating-point constant too large for type 'double'; maximum is 1.797693134862316E+308 [-Wliteral-range]
  double abstol = -1e500; // infinity
                   ^
normexp.c:167:78: warning: passing 'void (*)()' to parameter of type 'void *' converts between void pointer and function pointer [-Wpedantic]
  nmmin(3, par, parsOut, Fmin, normexp_m2loglik_saddle, fail, abstol, intol, &ex, alpha, beta, gamma, trace, fncount, maxit);
                                                                             ^˜˜
/Library/Frameworks/R.framework/Resources/include/R_ext/Applic.h:69:51: note: passing argument to parameter 'ex' here
           int *fail, double abstol, double intol, void *ex,
                                                         ^
2 warnings generated.
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o limma.so normexp.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/limma.buildbin-libdir/limma/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (limma)


>>>>>>> 
>>>>>>> FIXING LINKS FOR limma.buildbin-libdir/limma/libs//limma.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libgcc_s.1.dylib" "limma.buildbin-libdir/limma/libs//limma.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libgfortran.2.dylib" "limma.buildbin-libdir/limma/libs//limma.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libreadline.5.2.dylib" "limma.buildbin-libdir/limma/libs//limma.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libreadline.dylib" "limma.buildbin-libdir/limma/libs//limma.so"