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###
### Running command:
###
###   rm -rf snapCGH.buildbin-libdir && mkdir snapCGH.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh snapCGH_1.62.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R snapCGH.buildbin-libdir
###
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=snapCGH.buildbin-libdir snapCGH_1.62.0.tar.gz'
>>>>>>> 

* installing *source* package ‘snapCGH’ ...
** using staged installation
** libs
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c optimizer.c -o optimizer.o
optimizer.c:26:23: warning: unused variable 'temp2' [-Wunused-variable]
  double denom, temp, temp2, temp3;
                      ^
optimizer.c:26:10: warning: unused variable 'denom' [-Wunused-variable]
  double denom, temp, temp2, temp3;
         ^
optimizer.c:26:30: warning: unused variable 'temp3' [-Wunused-variable]
  double denom, temp, temp2, temp3;
                             ^
optimizer.c:194:69: warning: unused variable 'alphahat' [-Wunused-variable]
  double gammaA[3][3], gammaB[3][3], gammaC[3][3], alpha[3][nrow1], alphahat[3][nrow1], emis_prob[3][nrow1];
                                                                    ^
optimizer.c:195:30: warning: unused variable 'temp3' [-Wunused-variable]
  double denom, temp, temp2, temp3;
                             ^
optimizer.c:195:23: warning: unused variable 'temp2' [-Wunused-variable]
  double denom, temp, temp2, temp3;
                      ^
optimizer.c:195:10: warning: unused variable 'denom' [-Wunused-variable]
  double denom, temp, temp2, temp3;
         ^
optimizer.c:413:30: warning: unused variable 'temp3' [-Wunused-variable]
  double denom, temp, temp2, temp3;
                             ^
optimizer.c:413:23: warning: unused variable 'temp2' [-Wunused-variable]
  double denom, temp, temp2, temp3;
                      ^
optimizer.c:412:69: warning: unused variable 'alphahat' [-Wunused-variable]
  double gammaA[4][4], gammaB[4][4], gammaC[4][4], alpha[4][nrow1], alphahat[4][nrow1], emis_prob[4][nrow1];
                                                                    ^
optimizer.c:413:10: warning: unused variable 'denom' [-Wunused-variable]
  double denom, temp, temp2, temp3;
         ^
optimizer.c:686:69: warning: unused variable 'alphahat' [-Wunused-variable]
  double gammaA[5][5], gammaB[5][5], gammaC[5][5], alpha[5][nrow1], alphahat[5][nrow1], emis_prob[5][nrow1];
                                                                    ^
optimizer.c:687:10: warning: unused variable 'denom' [-Wunused-variable]
  double denom, temp, temp2, temp3;
         ^
optimizer.c:687:23: warning: unused variable 'temp2' [-Wunused-variable]
  double denom, temp, temp2, temp3;
                      ^
optimizer.c:687:30: warning: unused variable 'temp3' [-Wunused-variable]
  double denom, temp, temp2, temp3;
                             ^
15 warnings generated.
clang -mmacosx-version-min=10.13 -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 snapCGH.so optimizer.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.13-bioc/meat/snapCGH.buildbin-libdir/00LOCK-snapCGH/00new/snapCGH/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 (snapCGH)


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

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libgcc_s.1.dylib" "snapCGH.buildbin-libdir/snapCGH/libs/snapCGH.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libgfortran.5.dylib" "snapCGH.buildbin-libdir/snapCGH/libs/snapCGH.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libquadmath.0.dylib" "snapCGH.buildbin-libdir/snapCGH/libs/snapCGH.so"