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###
### Running command:
###
###   rm -rf iscream.buildbin-libdir && mkdir iscream.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh iscream_1.0.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R iscream.buildbin-libdir
###
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=iscream.buildbin-libdir iscream_1.0.0.tar.gz'
>>>>>>> 

* installing *source* package ‘iscream’ ...
** this is package ‘iscream’ version ‘1.0.0’
** using staged installation
*** Configuring for package installation...
**** Trying pkg-config to use system htslib headers...
     Falling back to Rhtslib
     Using Rhtslib cflags and libs for htslib!
**** Using clang
     Apple clang version 15.0.0 (clang-1500.1.0.2.5)
     Target: arm64-apple-darwin22.6.0
     Thread model: posix
     InstalledDir: /Library/Developer/CommandLineTools/usr/bin
     WARNING: Could not find pkg-config to check for minimum htslib version - make sure its >= 1.17
**** Compilation flags
     Using PKG_CFLAGS=-D_FILE_OFFSET_BITS=64
     Using PKG_LIBS='/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/usrlib/libhts.a' -lcurl -lbz2 -llzma -lz
**** Checking if htslib was compiled with libdeflate
     NOTE: iscream queries may be slower with Rhtslib than with htslib compiled with libdeflate
     See <https://huishenlab.github.io/iscream/articles/htslib.html> for more information
**** Success!
** libs
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using C++17
using SDK: ‘MacOSX11.3.1.sdk’
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppProgress/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppSpdlog/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/stringfish/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppProgress/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppSpdlog/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/stringfish/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c decode_mat.cpp -o decode_mat.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppProgress/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppSpdlog/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/stringfish/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c get_threads.cpp -o get_threads.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppProgress/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppSpdlog/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/stringfish/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c log.cpp -o log.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppProgress/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppSpdlog/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/stringfish/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c parsers.cpp -o parsers.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppProgress/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppSpdlog/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/stringfish/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c query.cpp -o query.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppProgress/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppSpdlog/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/stringfish/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c query_all.cpp -o query_all.o
In file included from query_all.cpp:1:
./query_all.hpp:56:1: warning: unused function 'khmap_destroy' [-Wunused-function]
KHASHL_MAP_INIT(static, khmap_t, khmap, CpG, int, kh_hash_cpg, kh_eq_cpg);
^
./../inst/include/khashl.h:350:13: note: expanded from macro 'KHASHL_MAP_INIT'
        SCOPE void prefix##_destroy(HType *h) { prefix##_m_destroy(h); } \
                   ^
<scratch space>:394:1: note: expanded from here
khmap_destroy
^
In file included from query_all.cpp:1:
./query_all.hpp:56:1: warning: unused function 'khmap_del' [-Wunused-function]
./../inst/include/khashl.h:352:12: note: expanded from macro 'KHASHL_MAP_INIT'
        SCOPE int prefix##_del(HType *h, khint_t k) { return prefix##_m_del(h, k); } \
                  ^
<scratch space>:399:1: note: expanded from here
khmap_del
^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppProgress/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppSpdlog/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/stringfish/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c summarize_regions.cpp -o summarize_regions.o
clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o iscream.so RcppExports.o decode_mat.o get_threads.o log.o parsers.o query.o query_all.o summarize_regions.o /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz -F/Library/Frameworks/R.framework/.. -framework R
installing to /Users/biocbuild/bbs-3.22-bioc/meat/iscream.buildbin-libdir/00LOCK-iscream/00new/iscream/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (iscream)


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

>>>>>>> Paths before fix:
iscream.buildbin-libdir/iscream/libs/iscream.so:
	iscream.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 1.0.5)
	/usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.11)
	/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.1)
	/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)

>>>>>>> Fix with install_name_tool:
install_name_tool -change "/usr/local/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libgcc_s.1.1.dylib" "iscream.buildbin-libdir/iscream/libs/iscream.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libgfortran.5.dylib" "iscream.buildbin-libdir/iscream/libs/iscream.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libquadmath.0.dylib" "iscream.buildbin-libdir/iscream/libs/iscream.so"

>>>>>>> Paths after fix:
iscream.buildbin-libdir/iscream/libs/iscream.so:
	iscream.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 1.0.5)
	/usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.11)
	/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.1)
	/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)