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###
### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL msa
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library’
* installing *source* package ‘msa’ ...
** using staged installation
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include  -I"./gc-7.2/include" -I"./Muscle/" -I"./ClustalW/src" -I"./ClustalOmega/src" -fPIC  -falign-functions=64 -Wall -g -O2  -c R_init_msa.cpp -o R_init_msa.o
In file included from R_init_msa.cpp:1:
In file included from ./ClustalOmega/src/RClustalOmega.h:4:
In file included from /Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
            SEXP data = Parent::get__();
                 ^
In file included from R_init_msa.cpp:3:
In file included from ./Muscle/RMuscle.h:4:
./Muscle/muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined]
#define assert(exp)     ((void)0)
        ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from R_init_msa.cpp:3:
In file included from ./Muscle/RMuscle.h:4:
In file included from ./Muscle/muscle.h:38:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
3 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include  -I"./gc-7.2/include" -I"./Muscle/" -I"./ClustalW/src" -I"./ClustalOmega/src" -fPIC  -falign-functions=64 -Wall -g -O2  -c SplitCharVector2List.cpp -o SplitCharVector2List.o
In file included from SplitCharVector2List.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
            SEXP data = Parent::get__();
                 ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include  -I"./gc-7.2/include" -I"./Muscle/" -I"./ClustalW/src" -I"./ClustalOmega/src" -fPIC  -falign-functions=64 -Wall -g -O2  -c SplitCharVector2Matrix.cpp -o SplitCharVector2Matrix.o
In file included from SplitCharVector2Matrix.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
            SEXP data = Parent::get__();
                 ^
1 warning generated.
make --file=msaMakefile --directory=gc-7.2
./configure --enable-cplusplus --enable-threads=pthreads --enable-shared --with-pic
checking build system type... arm-apple-darwin20.1.0
checking host system type... arm-apple-darwin20.1.0
checking target system type... arm-apple-darwin20.1.0
checking GC version numbers... major=7 minor=2 
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... ./install-sh -c -d
checking for gawk... no
checking for mawk... no
checking for nawk... no
checking for awk... awk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking whether to enable maintainer-specific portions of Makefiles... no
checking for style of include used by make... GNU
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc understands -c and -o together... yes
checking dependency style of gcc... gcc3
checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking dependency style of g++... gcc3
checking dependency style of gcc... gcc3
checking for inline... inline
checking for pthread_self in -lpthread... yes
configure: WARNING: "Explicit GC_INIT() calls may be required."
checking for xlc... no
checking whether gcc supports -fno-strict-aliasing... yes
checking whether to build shared libraries... yes
checking which machine-dependent code should be used... 
checking how to print strings... printf
checking for a sed that does not truncate output... /usr/bin/sed
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for fgrep... /usr/bin/grep -F
checking for ld used by gcc... /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld
checking if the linker (/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld) is GNU ld... no
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 786432
checking how to convert arm-apple-darwin20.1.0 file names to arm-apple-darwin20.1.0 format... func_convert_file_noop
checking how to convert arm-apple-darwin20.1.0 file names to toolchain format... func_convert_file_noop
checking for /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for ar... ar
checking for archiver @FILE support... no
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for sysroot... no
checking for mt... no
checking if : is a manifest tool... no
checking for dsymutil... dsymutil
checking for nmedit... nmedit
checking for lipo... lipo
checking for otool... otool
checking for otool64... no
checking for -single_module linker flag... yes
checking for -exported_symbols_list linker flag... yes
checking for -force_load linker flag... yes
checking how to run the C preprocessor... gcc -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for dlfcn.h... yes
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... yes
checking for gcc option to produce PIC... -fno-common -DPIC
checking if gcc PIC flag -fno-common -DPIC works... yes
checking if gcc static flag -static works... no
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... darwin20.1.0 dyld
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
checking how to run the C++ preprocessor... g++ -E
checking for ld used by g++... /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld
checking if the linker (/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld) is GNU ld... no
checking whether the g++ linker (/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld) supports shared libraries... yes
checking for g++ option to produce PIC... -fno-common -DPIC
checking if g++ PIC flag -fno-common -DPIC works... yes
checking if g++ static flag -static works... no
checking if g++ supports -c -o file.o... yes
checking if g++ supports -c -o file.o... (cached) yes
checking whether the g++ linker (/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... darwin20.1.0 dyld
checking how to hardcode library paths into programs... immediate
checking whether Solaris gcc optimization fix is necessary... no
checking sys/dg_sys_info.h usability... no
checking sys/dg_sys_info.h presence... no
checking for sys/dg_sys_info.h... no
checking for pkg-config... /opt/R/arm64/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for ATOMIC_OPS... no
checking which libatomic_ops to use... internal
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating bdw-gc.pc
config.status: creating include/private/config.h
config.status: executing depfiles commands
config.status: executing libtool commands
config.status: executing default commands
=== configuring in libatomic_ops (/Users/biocbuild/bbs-3.13-bioc/meat/msa/src/gc-7.2/libatomic_ops)
configure: running /bin/sh ./configure --disable-option-checking '--prefix=/usr/local'  '--enable-cplusplus' '--enable-threads=pthreads' '--enable-shared' '--with-pic' --cache-file=/dev/null --srcdir=.
checking build system type... arm-apple-darwin20.1.0
checking host system type... arm-apple-darwin20.1.0
checking target system type... arm-apple-darwin20.1.0
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... ./install-sh -c -d
checking for gawk... no
checking for mawk... no
checking for nawk... no
checking for awk... awk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking for ranlib... ranlib
checking for style of include used by make... GNU
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc understands -c and -o together... yes
checking dependency style of gcc... gcc3
checking dependency style of gcc... gcc3
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for stdlib.h... (cached) yes
checking for unistd.h... (cached) yes
checking for sys/param.h... yes
checking for getpagesize... yes
checking for working mmap... yes
checking for ANSI C header files... (cached) yes
checking for PIC compiler flag... -fPIC
checking whether gcc -fPIC causes __PIC__ definition... yes
checking for pthread_self in -lpthread... yes
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating pkgconfig/atomic_ops.pc
config.status: creating pkgconfig/atomic_ops-uninstalled.pc
config.status: creating doc/Makefile
config.status: creating src/Makefile
config.status: creating src/atomic_ops/Makefile
config.status: creating src/atomic_ops/sysdeps/Makefile
config.status: creating tests/Makefile
config.status: creating src/config.h
config.status: executing depfiles commands
config.status: executing default commands
make
depbase=`echo allchblk.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
	/bin/sh ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src  -fexceptions -g -O2 -fno-strict-aliasing -MT allchblk.lo -MD -MP -MF $depbase.Tpo -c -o allchblk.lo allchblk.c &&\
	mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT allchblk.lo -MD -MP -MF .deps/allchblk.Tpo -c allchblk.c  -fno-common -DPIC -o .libs/allchblk.o
In file included from allchblk.c:17:
In file included from ./include/private/gc_priv.h:94:
./include/private/gcconfig.h:523:5: error: "The collector has not been ported to this machine/OS combination."
#   error "The collector has not been ported to this machine/OS combination."
    ^
./include/private/gcconfig.h:2436:3: error: --> undefined ALIGNMENT
# error --> undefined ALIGNMENT
  ^
In file included from allchblk.c:17:
./include/private/gc_priv.h:520:7: error: define GC_THREAD_STATE_T
#     error define GC_THREAD_STATE_T
      ^
3 errors generated.
make[3]: *** [allchblk.lo] Error 1
make[2]: *** [all-recursive] Error 1
make[1]: *** [build_gc] Error 2
make: *** [build_gc] Error 2
ERROR: compilation failed for package ‘msa’
* removing ‘/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/msa’