##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf h5vc.buildbin-libdir && mkdir h5vc.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh h5vc_2.45.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R h5vc.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=h5vc.buildbin-libdir h5vc_2.45.0.tar.gz'
>>>>>>> 

* installing *source* package ‘h5vc’ ...
** this is package ‘h5vc’ version ‘2.45.0’
** using staged installation
** libs
using C compiler: ‘Apple clang version 17.0.0 (clang-1700.6.4.2)’
using C++ compiler: ‘Apple clang version 17.0.0 (clang-1700.6.4.2)’
using SDK: ‘MacOSX26.2.sdk’
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rhtslib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c bam_plbuf.c -o bam_plbuf.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rhtslib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c tallyBAM.cpp -o tallyBAM.o
tallyBAM.cpp:47:7: warning: unused variable 'len' [-Wunused-variable]
   47 |   int len = nttable->end - nttable->beg;
      |       ^~~
tallyBAM.cpp:60:18: warning: variable 'c' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
   60 |         }else if(p->indel > 0){
      |                  ^~~~~~~~~~~~
tallyBAM.cpp:64:16: note: uninitialized use occurs here
   64 |         str += c;
      |                ^
tallyBAM.cpp:60:15: note: remove the 'if' if its condition is always true
   60 |         }else if(p->indel > 0){
      |               ^~~~~~~~~~~~~~~~
tallyBAM.cpp:55:15: note: initialize the variable 'c' to silence this warning
   55 |         char c;
      |               ^
      |                = '\0'
tallyBAM.cpp:96:7: warning: unused variable 'len' [-Wunused-variable]
   96 |   int len = nttable->end - nttable->beg;
      |       ^~~
tallyBAM.cpp:140:6: warning: unused variable 'c' [-Wunused-variable]
  140 |         int c = 0;
      |             ^
tallyBAM.cpp:43:12: warning: unused function 'pileup_func_old' [-Wunused-function]
   43 | static int pileup_func_old(uint32_t tid, hts_pos_t pos, int n, const bam_pileup1_t *pl, void *data)
      |            ^~~~~~~~~~~~~~~
5 warnings generated.
clang++ -arch arm64 -std=gnu++20 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o h5vc.so bam_plbuf.o tallyBAM.o /Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz -F/Library/Frameworks/R.framework/.. -framework R
installing to /Users/biocbuild/bbs-3.23-bioc/meat/h5vc.buildbin-libdir/00LOCK-h5vc/00new/h5vc/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 (h5vc)


>>>>>>> 
>>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR h5vc.buildbin-libdir/h5vc/libs/h5vc.so
>>>>>>> 

>>>>>>> Paths before fix:
h5vc.buildbin-libdir/h5vc/libs/h5vc.so:
	h5vc.so (compatibility version 0.0.0, current version 0.0.0)
	/usr/lib/libcurl.4.dylib (compatibility version 7.0.0, current version 9.0.0)
	/usr/lib/libbz2.1.0.dylib (compatibility version 1.0.0, current version 1.0.8)
	/usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.12)
	/Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libR.dylib (compatibility version 4.6.0, current version 4.6.0)
	/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 2000.67.0)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1356.0.0)

>>>>>>> Fix with install_name_tool:
ERROR: R installation problem: File /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/lib/libR.dylib not found!