Package: DeMixT

Version: 1.3.1

Command: rm -rf DeMixT.buildbin-libdir && mkdir DeMixT.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh DeMixT_1.3.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R DeMixT.buildbin-libdir

StartedAt: 2020-01-16 10:46:32 -0500 (Thu, 16 Jan 2020)

EndedAt: 2020-01-16 10:47:11 -0500 (Thu, 16 Jan 2020)

EllapsedTime: 39.3 seconds

RetCode: 0

Status:  OK

PackageFile: DeMixT_1.3.1.tgz

PackageFileSize: 1.924 MiB

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### Running command:
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###   rm -rf DeMixT.buildbin-libdir && mkdir DeMixT.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh DeMixT_1.3.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R DeMixT.buildbin-libdir
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=DeMixT.buildbin-libdir DeMixT_1.3.1.tar.gz'
>>>>>>> 

* installing *source* package ‘DeMixT’ ...
** using staged installation
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c DeMixT.c -o DeMixT.o
DeMixT.c:255:26: warning: implicit declaration of function 'Rprintf' is invalid in C99 [-Wimplicit-function-declaration]
      if (nHavepi != 1)  Rprintf("Iteration %d: updating purities\n", i+1);
                         ^
DeMixT.c:436:21: warning: implicit declaration of function 'Rprintf' is invalid in C99 [-Wimplicit-function-declaration]
  if (nHavepi != 1) Rprintf("There are  %d normals and %d tumors\n", fNorm,intx);
                    ^
2 warnings generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c init.c -o init.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c registerDynamicSymbol.c -o registerDynamicSymbol.o
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 DeMixT.so DeMixT.o init.o registerDynamicSymbol.o -fopenmp -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.11-bioc/meat/DeMixT.buildbin-libdir/00LOCK-DeMixT/00new/DeMixT/libs
** R
** data
*** moving datasets to lazyload DB
** 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 (DeMixT)


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

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libgcc_s.1.dylib" "DeMixT.buildbin-libdir/DeMixT/libs//DeMixT.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libgfortran.3.dylib" "DeMixT.buildbin-libdir/DeMixT/libs//DeMixT.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libreadline.5.2.dylib" "DeMixT.buildbin-libdir/DeMixT/libs//DeMixT.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libreadline.dylib" "DeMixT.buildbin-libdir/DeMixT/libs//DeMixT.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libquadmath.0.dylib" "DeMixT.buildbin-libdir/DeMixT/libs//DeMixT.so"