##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf PICS.buildbin-libdir && mkdir PICS.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh PICS_2.42.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R PICS.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=PICS.buildbin-libdir PICS_2.42.0.tar.gz'
>>>>>>> 

* installing *source* package ‘PICS’ ...
** using staged installation
checking for pkg-config... /opt/homebrew/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for GSL... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c pics.c -o pics.o
pics.c:1009:9: warning: variable 'chiSum' set but not used [-Wunused-but-set-variable]
        double chiSum, etaF, etaR, dd, cc;
               ^
pics.c:1301:3: warning: variable 'penalty' is used uninitialized whenever switch default is taken [-Wsometimes-uninitialized]
                default:
                ^~~~~~~
pics.c:1307:97: note: uninitialized use occurs here
        bic = logDensityMix(yF, w, muF, sigmaSqF, K, NF) + logDensityMix(yR, w, muR, sigmaSqR, K,NR) - penalty;
                                                                                                       ^~~~~~~
pics.c:1275:42: note: initialize the variable 'penalty' to silence this warning
        double bic, tmp, muF[K], muR[K], penalty, distance;
                                                ^
                                                 = 0.0
pics.c:1633:76: warning: unused variable 'PhiRw' [-Wunused-variable]
          double aNormF, aNormR, bNormF, bNormR, P0F=1, P0R=1, PhiF, PhiR, PhiFw, PhiRw, wPjF, wPjR; 
                                                                                  ^
pics.c:1633:69: warning: unused variable 'PhiFw' [-Wunused-variable]
          double aNormF, aNormR, bNormF, bNormR, P0F=1, P0R=1, PhiF, PhiR, PhiFw, PhiRw, wPjF, wPjR; 
                                                                           ^
pics.c:1889:11: warning: unused variable 'j' [-Wunused-variable]
  int i=0,j=0,k=0,l=0,kMerge=0,flag=0;
          ^
pics.c:1889:7: warning: unused variable 'i' [-Wunused-variable]
  int i=0,j=0,k=0,l=0,kMerge=0,flag=0;
      ^
6 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c segment.c -o segment.o
segment.c:406:6: warning: variable 'pp' is incremented both in the loop header and in the loop body [-Wfor-loop-analysis]
                                        pp++;
                                        ^
segment.c:395:27: note: incremented here
                                for (pp=start; pp<=p; pp++) {
                                                      ^
segment.c:536:6: warning: variable 'pp' is incremented both in the loop header and in the loop body [-Wfor-loop-analysis]
                                        pp++;
                                        ^
segment.c:525:27: note: incremented here
                                for (pp=start; pp<=p; pp++) {
                                                      ^
segment.c:1490:8: warning: unused variable 'filter1' [-Wunused-variable]
  SEXP filter1;
       ^
segment.c:1489:11: warning: unused variable 'muFilter' [-Wunused-variable]
  double *muFilter, *deltaFilter, *sFFilter, *sRFilter, *seFilter, *seFilterF, *seFilterR, *scoreFilter, *score;
          ^
segment.c:1494:19: warning: variable 'chr' set but not used [-Wunused-but-set-variable]
  SEXP ans, x, y, chr, names;
                  ^
5 warnings generated.
clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o PICS.so pics.o segment.o -L/usr/local/lib -lgsl -lgslcblas -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: -undefined dynamic_lookup may not work with chained fixups
installing to /Volumes/External/bbs-3.16-bioc-m1/meat/PICS.buildbin-libdir/00LOCK-PICS/00new/PICS/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 (PICS)


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

install_name_tool -change "/opt/R/arm64/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libgcc_s.1.1.dylib" "PICS.buildbin-libdir/PICS/libs/PICS.so"
install_name_tool -change "/opt/R/arm64/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libgfortran.5.dylib" "PICS.buildbin-libdir/PICS/libs/PICS.so"
install_name_tool -change "/opt/R/arm64/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libquadmath.0.dylib" "PICS.buildbin-libdir/PICS/libs/PICS.so"