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###
### Running command:
###
###   rm -rf qpgraph.buildbin-libdir && mkdir qpgraph.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh qpgraph_2.36.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R qpgraph.buildbin-libdir
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=qpgraph.buildbin-libdir qpgraph_2.36.0.tar.gz'
>>>>>>> 

* installing *source* package ‘qpgraph’ ...
** using staged installation
checking for gcc... clang -arch arm64
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether clang -arch arm64 accepts -g... yes
checking for clang -arch arm64 option to accept ANSI C... none needed
checking build system type... aarch64-apple-darwin22.6.0
checking host system type... aarch64-apple-darwin22.6.0
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_FC_LEN_T  -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2 -Wall -pedantic -fPIC  -falign-functions=64 -Wall -g -O2  -c cliquer.c -o cliquer.o
cliquer.c:13:46: warning: invalid UTF-8 in comment [-Winvalid-utf8]
 * Copyright (C) 2002 Sampo Niskanen, Patric <D6>sterg<E5>rd.
                                             ^
cliquer.c:13:52: warning: invalid UTF-8 in comment [-Winvalid-utf8]
 * Copyright (C) 2002 Sampo Niskanen, Patric <D6>sterg<E5>rd.
                                                      ^
In file included from cliquer.c:29:
In file included from ./cliquer.h:7:
./set.h:12:46: warning: invalid UTF-8 in comment [-Winvalid-utf8]
 * Copyright (C) 2002 Sampo Niskanen, Patric <D6>sterg<E5>rd.
                                             ^
./set.h:12:52: warning: invalid UTF-8 in comment [-Winvalid-utf8]
 * Copyright (C) 2002 Sampo Niskanen, Patric <D6>sterg<E5>rd.
                                                      ^
4 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_FC_LEN_T  -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2 -Wall -pedantic -fPIC  -falign-functions=64 -Wall -g -O2  -c graph.c -o graph.o
graph.c:12:46: warning: invalid UTF-8 in comment [-Winvalid-utf8]
 * Copyright (C) 2002 Sampo Niskanen, Patric <D6>sterg<E5>rd.
                                             ^
graph.c:12:52: warning: invalid UTF-8 in comment [-Winvalid-utf8]
 * Copyright (C) 2002 Sampo Niskanen, Patric <D6>sterg<E5>rd.
                                                      ^
In file included from graph.c:28:
In file included from ./graph.h:5:
./set.h:12:46: warning: invalid UTF-8 in comment [-Winvalid-utf8]
 * Copyright (C) 2002 Sampo Niskanen, Patric <D6>sterg<E5>rd.
                                             ^
./set.h:12:52: warning: invalid UTF-8 in comment [-Winvalid-utf8]
 * Copyright (C) 2002 Sampo Niskanen, Patric <D6>sterg<E5>rd.
                                                      ^
4 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_FC_LEN_T  -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2 -Wall -pedantic -fPIC  -falign-functions=64 -Wall -g -O2  -c qpgraph.c -o qpgraph.o
qpgraph.c:24:9: warning: 'USE_FC_LEN_T' macro redefined [-Wmacro-redefined]
#define USE_FC_LEN_T
        ^
<command line>:2:9: note: previous definition is here
#define USE_FC_LEN_T 1
        ^
In file included from qpgraph.c:39:
In file included from ./cliquer.h:7:
./set.h:12:46: warning: invalid UTF-8 in comment [-Winvalid-utf8]
 * Copyright (C) 2002 Sampo Niskanen, Patric <D6>sterg<E5>rd.
                                             ^
./set.h:12:52: warning: invalid UTF-8 in comment [-Winvalid-utf8]
 * Copyright (C) 2002 Sampo Niskanen, Patric <D6>sterg<E5>rd.
                                                      ^
qpgraph.c:5176:10: warning: variable 'avgpr' set but not used [-Wunused-but-set-variable]
  double avgpr = 0;
         ^
4 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -DUSE_FC_LEN_T  -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2 -Wall -pedantic -fPIC  -falign-functions=64 -Wall -g -O2  -c reorder.c -o reorder.o
reorder.c:12:46: warning: invalid UTF-8 in comment [-Winvalid-utf8]
 * Copyright (C) 2002 Sampo Niskanen, Patric <D6>sterg<E5>rd.
                                             ^
reorder.c:12:52: warning: invalid UTF-8 in comment [-Winvalid-utf8]
 * Copyright (C) 2002 Sampo Niskanen, Patric <D6>sterg<E5>rd.
                                                      ^
In file included from reorder.c:19:
In file included from ./reorder.h:5:
./set.h:12:46: warning: invalid UTF-8 in comment [-Winvalid-utf8]
 * Copyright (C) 2002 Sampo Niskanen, Patric <D6>sterg<E5>rd.
                                             ^
./set.h:12:52: warning: invalid UTF-8 in comment [-Winvalid-utf8]
 * Copyright (C) 2002 Sampo Niskanen, Patric <D6>sterg<E5>rd.
                                                      ^
4 warnings generated.
clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o qpgraph.so cliquer.o graph.o qpgraph.o reorder.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lemutls_w -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/qpgraph.buildbin-libdir/00LOCK-qpgraph/00new/qpgraph/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for ‘det’ from package ‘Matrix’ in package ‘qpgraph’
** 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 (qpgraph)


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

>>>>>>> Paths before fix:
qpgraph.buildbin-libdir/qpgraph/libs/qpgraph.so:
	qpgraph.so (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib (compatibility version 4.3.0, current version 4.3.3)
	/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRblas.dylib (compatibility version 0.0.0, current version 0.0.0)
	/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0/libgfortran.5.dylib (compatibility version 6.0.0, current version 6.0.0)
	/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0/libquadmath.0.dylib (compatibility version 1.0.0, current version 1.0.0)
	/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.3)
	/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
	/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/4.3-arm64/Resources/lib/libgcc_s.1.1.dylib" "qpgraph.buildbin-libdir/qpgraph/libs/qpgraph.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libgfortran.5.dylib" "qpgraph.buildbin-libdir/qpgraph/libs/qpgraph.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libquadmath.0.dylib" "qpgraph.buildbin-libdir/qpgraph/libs/qpgraph.so"
install_name_tool -change "/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libgfortran.5.dylib" "qpgraph.buildbin-libdir/qpgraph/libs/qpgraph.so"
install_name_tool -change "/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libquadmath.0.dylib" "qpgraph.buildbin-libdir/qpgraph/libs/qpgraph.so"

>>>>>>> Paths after fix:
qpgraph.buildbin-libdir/qpgraph/libs/qpgraph.so:
	qpgraph.so (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib (compatibility version 4.3.0, current version 4.3.3)
	/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRblas.dylib (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libgfortran.5.dylib (compatibility version 6.0.0, current version 6.0.0)
	/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libquadmath.0.dylib (compatibility version 1.0.0, current version 1.0.0)
	/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.3)
	/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)