############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf msa.buildbin-libdir && mkdir msa.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh msa_1.36.1.tar.gz /Library/Frameworks/R.framework/Resources/bin/R msa.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=msa.buildbin-libdir msa_1.36.1.tar.gz' >>>>>>> * installing *source* package ‘msa’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I"./gc-8.2.2/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: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) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.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) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I"./gc-8.2.2/include" -I"./Muscle/" -I"./ClustalW/src" -I"./ClustalOmega/src" -fPIC -falign-functions=64 -Wall -g -O2 -c SplitCharVector2List.cpp -o SplitCharVector2List.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I"./gc-8.2.2/include" -I"./Muscle/" -I"./ClustalW/src" -I"./ClustalOmega/src" -fPIC -falign-functions=64 -Wall -g -O2 -c SplitCharVector2Matrix.cpp -o SplitCharVector2Matrix.o make --file=msaMakefile --directory=gc-8.2.2 ./configure --enable-cplusplus --enable-threads=pthreads --enable-shared=no --with-pic checking build system type... aarch64-apple-darwin22.6.0 checking host system type... aarch64-apple-darwin22.6.0 checking target system type... aarch64-apple-darwin22.6.0 checking GC version numbers... major=8 minor=2 micro=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 whether make supports the include directive... yes (GNU style) 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 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... /Library/Developer/CommandLineTools/usr/bin/ld checking if the linker (/Library/Developer/CommandLineTools/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 aarch64-apple-darwin22.6.0 file names to aarch64-apple-darwin22.6.0 format... func_convert_file_noop checking how to convert aarch64-apple-darwin22.6.0 file names to toolchain format... func_convert_file_noop checking for /Library/Developer/CommandLineTools/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 a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 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... ld: warning: -single_module is obsolete no 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 (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... darwin22.6.0 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... no checking whether to build static libraries... yes checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /Library/Developer/CommandLineTools/usr/bin/ld checking if the linker (/Library/Developer/CommandLineTools/usr/bin/ld) is GNU ld... no checking whether the g++ linker (/Library/Developer/CommandLineTools/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 (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... darwin22.6.0 dyld checking how to hardcode library paths into programs... immediate checking for emscripten... no checking for inline... inline configure: WARNING: "Explicit GC_INIT() calls may be required." checking for pthread_self in -lpthread... yes checking for clock_gettime without additional libraries... yes checking whether compiler supports -Wextra... yes checking whether compiler supports -Wpedantic... yes checking for xlc... no checking whether compiler supports -fno-strict-aliasing... yes checking for getcontext... yes checking for dl_iterate_phdr... no checking execinfo.h usability... yes checking execinfo.h presence... yes checking for execinfo.h... yes checking whether to build shared libraries... no checking which machine-dependent code should be used... checking whether AIX gcc optimization fix is necessary... no checking whether -Wno-frame-address works... no checking for dladdr... yes checking for sigsetjmp... yes checking for pthread_setname_np... 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 compiler intrinsics support... yes checking which libatomic_ops to use... none 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/config.h config.status: include/config.h is unchanged config.status: executing depfiles commands config.status: executing libtool 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 -fexceptions -Wall -Wextra -Wpedantic -Wno-long-long -g -O2 -fno-strict-aliasing -MT allchblk.lo -MD -MP -MF $depbase.Tpo -c -o allchblk.lo allchblk.c &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -Wall -Wextra -Wpedantic -Wno-long-long -g -O2 -fno-strict-aliasing -MT allchblk.lo -MD -MP -MF .deps/allchblk.Tpo -c allchblk.c -fno-common -DPIC -o allchblk.o depbase=`echo alloc.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -Wall -Wextra -Wpedantic -Wno-long-long -g -O2 -fno-strict-aliasing -MT alloc.lo -MD -MP -MF $depbase.Tpo -c -o alloc.lo alloc.c &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -Wall -Wextra -Wpedantic -Wno-long-long -g -O2 -fno-strict-aliasing -MT alloc.lo -MD -MP -MF .deps/alloc.Tpo -c alloc.c -fno-common -DPIC -o alloc.o depbase=`echo blacklst.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -Wall -Wextra -Wpedantic -Wno-long-long -g -O2 -fno-strict-aliasing -MT blacklst.lo -MD -MP -MF $depbase.Tpo -c -o blacklst.lo blacklst.c &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -Wall -Wextra -Wpedantic -Wno-long-long -g -O2 -fno-strict-aliasing -MT blacklst.lo -MD -MP -MF .deps/blacklst.Tpo -c blacklst.c -fno-common -DPIC -o blacklst.o depbase=`echo dbg_mlc.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -Wall -Wextra -Wpedantic -Wno-long-long -g -O2 -fno-strict-aliasing -MT dbg_mlc.lo -MD -MP -MF $depbase.Tpo -c -o dbg_mlc.lo dbg_mlc.c &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -Wall -Wextra -Wpedantic -Wno-long-long -g -O2 -fno-strict-aliasing -MT dbg_mlc.lo -MD -MP -MF .deps/dbg_mlc.Tpo -c dbg_mlc.c -fno-common -DPIC -o dbg_mlc.o depbase=`echo dyn_load.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -Wall -Wextra -Wpedantic -Wno-long-long -g -O2 -fno-strict-aliasing -MT dyn_load.lo -MD -MP -MF $depbase.Tpo -c -o dyn_load.lo dyn_load.c &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -Wall -Wextra -Wpedantic -Wno-long-long -g -O2 -fno-strict-aliasing -MT dyn_load.lo -MD -MP -MF .deps/dyn_load.Tpo -c dyn_load.c -fno-common -DPIC -o dyn_load.o dyn_load.c:1497:12: warning: '_dyld_bind_fully_image_containing_address' is deprecated: first deprecated in macOS 10.5 - dlopen(RTLD_NOW) [-Wdeprecated-declarations] if (!_dyld_bind_fully_image_containing_address( ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/mach-o/dyld.h:259:13: note: '_dyld_bind_fully_image_containing_address' has been explicitly marked deprecated here extern bool _dyld_bind_fully_image_containing_address(const void* address) __API_UNAVAILABLE(ios, tvos, watchos) DYLD_DRIVERKIT_UNAVAILABLE __OSX_DEPRECATED(10.1, 10.5, "dlopen(RTLD_NOW)"); ^ 1 warning generated. depbase=`echo finalize.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -Wall -Wextra -Wpedantic -Wno-long-long -g -O2 -fno-strict-aliasing -MT finalize.lo -MD -MP -MF $depbase.Tpo -c -o finalize.lo finalize.c &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -Wall -Wextra -Wpedantic -Wno-long-long -g -O2 -fno-strict-aliasing -MT finalize.lo -MD -MP -MF .deps/finalize.Tpo -c finalize.c -fno-common -DPIC -o finalize.o depbase=`echo gc_dlopen.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -Wall -Wextra -Wpedantic -Wno-long-long -g -O2 -fno-strict-aliasing -MT gc_dlopen.lo -MD -MP -MF $depbase.Tpo -c -o gc_dlopen.lo gc_dlopen.c &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -Wall -Wextra -Wpedantic -Wno-long-long -g -O2 -fno-strict-aliasing -MT gc_dlopen.lo -MD -MP -MF .deps/gc_dlopen.Tpo -c gc_dlopen.c -fno-common -DPIC -o gc_dlopen.o depbase=`echo headers.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -Wall -Wextra -Wpedantic -Wno-long-long -g -O2 -fno-strict-aliasing -MT headers.lo -MD -MP -MF $depbase.Tpo -c -o headers.lo headers.c &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -Wall -Wextra -Wpedantic -Wno-long-long -g -O2 -fno-strict-aliasing -MT headers.lo -MD -MP -MF .deps/headers.Tpo -c headers.c -fno-common -DPIC -o headers.o depbase=`echo mach_dep.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -Wall -Wextra -Wpedantic -Wno-long-long -g -O2 -fno-strict-aliasing -MT mach_dep.lo -MD -MP -MF $depbase.Tpo -c -o mach_dep.lo mach_dep.c &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -Wall -Wextra -Wpedantic -Wno-long-long -g -O2 -fno-strict-aliasing -MT mach_dep.lo -MD -MP -MF .deps/mach_dep.Tpo -c mach_dep.c -fno-common -DPIC -o mach_dep.o depbase=`echo malloc.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -Wall -Wextra -Wpedantic -Wno-long-long -g -O2 -fno-strict-aliasing -MT malloc.lo -MD -MP -MF $depbase.Tpo -c -o malloc.lo malloc.c &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -Wall -Wextra -Wpedantic -Wno-long-long -g -O2 -fno-strict-aliasing -MT malloc.lo -MD -MP -MF .deps/malloc.Tpo -c malloc.c -fno-common -DPIC -o malloc.o depbase=`echo mallocx.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -Wall -Wextra -Wpedantic -Wno-long-long -g -O2 -fno-strict-aliasing -MT mallocx.lo -MD -MP -MF $depbase.Tpo -c -o mallocx.lo mallocx.c &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -Wall -Wextra -Wpedantic -Wno-long-long -g -O2 -fno-strict-aliasing -MT mallocx.lo -MD -MP -MF .deps/mallocx.Tpo -c mallocx.c -fno-common -DPIC -o mallocx.o depbase=`echo mark.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -Wall -Wextra -Wpedantic -Wno-long-long -g -O2 -fno-strict-aliasing -MT mark.lo -MD -MP -MF $depbase.Tpo -c -o mark.lo mark.c &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -Wall -Wextra -Wpedantic -Wno-long-long -g -O2 -fno-strict-aliasing -MT mark.lo -MD -MP -MF .deps/mark.Tpo -c mark.c -fno-common -DPIC -o mark.o depbase=`echo mark_rts.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -Wall -Wextra -Wpedantic -Wno-long-long -g -O2 -fno-strict-aliasing -MT mark_rts.lo -MD -MP -MF $depbase.Tpo -c -o mark_rts.lo mark_rts.c &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -Wall -Wextra -Wpedantic -Wno-long-long -g -O2 -fno-strict-aliasing -MT mark_rts.lo -MD -MP -MF .deps/mark_rts.Tpo -c mark_rts.c -fno-common -DPIC -o mark_rts.o depbase=`echo misc.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -Wall -Wextra -Wpedantic -Wno-long-long -g -O2 -fno-strict-aliasing -MT misc.lo -MD -MP -MF $depbase.Tpo -c -o misc.lo misc.c &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -Wall -Wextra -Wpedantic -Wno-long-long -g -O2 -fno-strict-aliasing -MT misc.lo -MD -MP -MF .deps/misc.Tpo -c misc.c -fno-common -DPIC -o misc.o depbase=`echo new_hblk.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -Wall -Wextra -Wpedantic -Wno-long-long -g -O2 -fno-strict-aliasing -MT new_hblk.lo -MD -MP -MF $depbase.Tpo -c -o new_hblk.lo new_hblk.c &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -Wall -Wextra -Wpedantic -Wno-long-long -g -O2 -fno-strict-aliasing -MT new_hblk.lo -MD -MP -MF .deps/new_hblk.Tpo -c new_hblk.c -fno-common -DPIC -o new_hblk.o depbase=`echo obj_map.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -Wall -Wextra -Wpedantic -Wno-long-long -g -O2 -fno-strict-aliasing -MT obj_map.lo -MD -MP -MF $depbase.Tpo -c -o obj_map.lo obj_map.c &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -Wall -Wextra -Wpedantic -Wno-long-long -g -O2 -fno-strict-aliasing -MT obj_map.lo -MD -MP -MF .deps/obj_map.Tpo -c obj_map.c -fno-common -DPIC -o obj_map.o depbase=`echo os_dep.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -Wall -Wextra -Wpedantic -Wno-long-long -g -O2 -fno-strict-aliasing -MT os_dep.lo -MD -MP -MF $depbase.Tpo -c -o os_dep.lo os_dep.c &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -Wall -Wextra -Wpedantic -Wno-long-long -g -O2 -fno-strict-aliasing -MT os_dep.lo -MD -MP -MF .deps/os_dep.Tpo -c os_dep.c -fno-common -DPIC -o os_dep.o depbase=`echo ptr_chck.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -Wall -Wextra -Wpedantic -Wno-long-long -g -O2 -fno-strict-aliasing -MT ptr_chck.lo -MD -MP -MF $depbase.Tpo -c -o ptr_chck.lo ptr_chck.c &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -Wall -Wextra -Wpedantic -Wno-long-long -g -O2 -fno-strict-aliasing -MT ptr_chck.lo -MD -MP -MF .deps/ptr_chck.Tpo -c ptr_chck.c -fno-common -DPIC -o ptr_chck.o depbase=`echo reclaim.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -Wall -Wextra -Wpedantic -Wno-long-long -g -O2 -fno-strict-aliasing -MT reclaim.lo -MD -MP -MF $depbase.Tpo -c -o reclaim.lo reclaim.c &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -Wall -Wextra -Wpedantic -Wno-long-long -g -O2 -fno-strict-aliasing -MT reclaim.lo -MD -MP -MF .deps/reclaim.Tpo -c reclaim.c -fno-common -DPIC -o reclaim.o depbase=`echo specific.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -Wall -Wextra -Wpedantic -Wno-long-long -g -O2 -fno-strict-aliasing -MT specific.lo -MD -MP -MF $depbase.Tpo -c -o specific.lo specific.c &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -Wall -Wextra -Wpedantic -Wno-long-long -g -O2 -fno-strict-aliasing -MT specific.lo -MD -MP -MF .deps/specific.Tpo -c specific.c -fno-common -DPIC -o specific.o depbase=`echo typd_mlc.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -Wall -Wextra -Wpedantic -Wno-long-long -g -O2 -fno-strict-aliasing -MT typd_mlc.lo -MD -MP -MF $depbase.Tpo -c -o typd_mlc.lo typd_mlc.c &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -Wall -Wextra -Wpedantic -Wno-long-long -g -O2 -fno-strict-aliasing -MT typd_mlc.lo -MD -MP -MF .deps/typd_mlc.Tpo -c typd_mlc.c -fno-common -DPIC -o typd_mlc.o depbase=`echo pthread_start.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -Wall -Wextra -Wpedantic -Wno-long-long -g -O2 -fno-strict-aliasing -MT pthread_start.lo -MD -MP -MF $depbase.Tpo -c -o pthread_start.lo pthread_start.c &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -Wall -Wextra -Wpedantic -Wno-long-long -g -O2 -fno-strict-aliasing -MT pthread_start.lo -MD -MP -MF .deps/pthread_start.Tpo -c pthread_start.c -fno-common -DPIC -o pthread_start.o depbase=`echo pthread_support.lo | sed 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-DHAVE_CONFIG_H -I./include -I./include -fexceptions -Wall -Wextra -Wpedantic -Wno-long-long -g -O2 -fno-strict-aliasing -MT darwin_stop_world.lo -MD -MP -MF .deps/darwin_stop_world.Tpo -c darwin_stop_world.c -fno-common -DPIC -o darwin_stop_world.o depbase=`echo thread_local_alloc.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -Wall -Wextra -Wpedantic -Wno-long-long -g -O2 -fno-strict-aliasing -MT thread_local_alloc.lo -MD -MP -MF $depbase.Tpo -c -o thread_local_alloc.lo thread_local_alloc.c &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -Wall -Wextra -Wpedantic -Wno-long-long -g -O2 -fno-strict-aliasing -MT thread_local_alloc.lo -MD -MP -MF .deps/thread_local_alloc.Tpo -c thread_local_alloc.c -fno-common -DPIC -o thread_local_alloc.o depbase=`echo gcj_mlc.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -Wall -Wextra -Wpedantic -Wno-long-long -g -O2 -fno-strict-aliasing -MT gcj_mlc.lo -MD -MP -MF $depbase.Tpo -c -o gcj_mlc.lo gcj_mlc.c &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -Wall -Wextra -Wpedantic -Wno-long-long -g -O2 -fno-strict-aliasing -MT gcj_mlc.lo -MD -MP -MF .deps/gcj_mlc.Tpo -c gcj_mlc.c -fno-common -DPIC -o gcj_mlc.o depbase=`echo fnlz_mlc.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -Wall -Wextra -Wpedantic -Wno-long-long -g -O2 -fno-strict-aliasing -MT fnlz_mlc.lo -MD -MP -MF $depbase.Tpo -c -o fnlz_mlc.lo fnlz_mlc.c &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -Wall -Wextra -Wpedantic -Wno-long-long -g -O2 -fno-strict-aliasing -MT fnlz_mlc.lo -MD -MP -MF .deps/fnlz_mlc.Tpo -c fnlz_mlc.c -fno-common -DPIC -o fnlz_mlc.o /bin/sh ./libtool --tag=CC --mode=link gcc -fexceptions -Wall -Wextra -Wpedantic -Wno-long-long -g -O2 -fno-strict-aliasing -Wl,-single_module -version-info 6:1:5 -no-undefined -o libgc.la -rpath /usr/local/lib allchblk.lo alloc.lo blacklst.lo dbg_mlc.lo dyn_load.lo finalize.lo gc_dlopen.lo headers.lo mach_dep.lo malloc.lo mallocx.lo mark.lo mark_rts.lo misc.lo new_hblk.lo obj_map.lo os_dep.lo ptr_chck.lo reclaim.lo specific.lo typd_mlc.lo pthread_start.lo pthread_support.lo darwin_stop_world.lo thread_local_alloc.lo gcj_mlc.lo fnlz_mlc.lo -lpthread libtool: link: ar cru .libs/libgc.a allchblk.o alloc.o blacklst.o dbg_mlc.o dyn_load.o finalize.o gc_dlopen.o headers.o mach_dep.o malloc.o mallocx.o mark.o mark_rts.o misc.o new_hblk.o obj_map.o os_dep.o ptr_chck.o reclaim.o specific.o typd_mlc.o pthread_start.o pthread_support.o darwin_stop_world.o thread_local_alloc.o gcj_mlc.o fnlz_mlc.o libtool: link: ranlib .libs/libgc.a libtool: link: ( cd ".libs" && rm -f "libgc.la" && ln -s "../libgc.la" "libgc.la" ) depbase=`echo gc_badalc.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I./include -I./include -fexceptions -Wall -Wextra -Wpedantic -Wno-long-long -g -O2 -MT gc_badalc.lo -MD -MP -MF $depbase.Tpo -c -o gc_badalc.lo gc_badalc.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I./include -I./include -fexceptions -Wall -Wextra -Wpedantic -Wno-long-long -g -O2 -MT gc_badalc.lo -MD -MP -MF .deps/gc_badalc.Tpo -c gc_badalc.cc -fno-common -DPIC -o gc_badalc.o depbase=`echo gc_cpp.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I./include -I./include -fexceptions -Wall -Wextra -Wpedantic -Wno-long-long -g -O2 -MT gc_cpp.lo -MD -MP -MF $depbase.Tpo -c -o gc_cpp.lo gc_cpp.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I./include -I./include -fexceptions -Wall -Wextra -Wpedantic -Wno-long-long -g -O2 -MT gc_cpp.lo -MD -MP -MF .deps/gc_cpp.Tpo -c gc_cpp.cc -fno-common -DPIC -o gc_cpp.o /bin/sh ./libtool --tag=CXX --mode=link g++ -fexceptions -Wall -Wextra -Wpedantic -Wno-long-long -g -O2 -version-info 6:0:5 -no-undefined -o libgccpp.la -rpath /usr/local/lib gc_badalc.lo gc_cpp.lo libgc.la libtool: link: ar cru .libs/libgccpp.a gc_badalc.o gc_cpp.o libtool: link: ranlib .libs/libgccpp.a libtool: link: ( cd ".libs" && rm -f "libgccpp.la" && ln -s "../libgccpp.la" "libgccpp.la" ) /bin/sh ./libtool --tag=CXX --mode=link g++ -fexceptions -Wall -Wextra -Wpedantic -Wno-long-long -g -O2 -version-info 6:0:5 -no-undefined -o libgctba.la -rpath /usr/local/lib gc_badalc.lo libgc.la libtool: link: ar cru .libs/libgctba.a gc_badalc.o libtool: link: ranlib .libs/libgctba.a libtool: link: ( cd ".libs" && rm -f "libgctba.la" && ln -s "../libgctba.la" "libgctba.la" ) /bin/sh ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -Wall -Wextra -Wpedantic -Wno-long-long -g -O2 -fno-strict-aliasing -MT cord/libcord_la-cordbscs.lo -MD -MP -MF cord/.deps/libcord_la-cordbscs.Tpo -c -o cord/libcord_la-cordbscs.lo `test -f 'cord/cordbscs.c' || echo './'`cord/cordbscs.c libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -Wall -Wextra -Wpedantic -Wno-long-long -g -O2 -fno-strict-aliasing -MT cord/libcord_la-cordbscs.lo -MD -MP -MF cord/.deps/libcord_la-cordbscs.Tpo -c cord/cordbscs.c -fno-common -DPIC -o cord/libcord_la-cordbscs.o mv -f cord/.deps/libcord_la-cordbscs.Tpo cord/.deps/libcord_la-cordbscs.Plo /bin/sh ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -Wall -Wextra -Wpedantic -Wno-long-long -g -O2 -fno-strict-aliasing -MT cord/libcord_la-cordprnt.lo -MD -MP -MF cord/.deps/libcord_la-cordprnt.Tpo -c -o cord/libcord_la-cordprnt.lo `test -f 'cord/cordprnt.c' || echo './'`cord/cordprnt.c libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -Wall -Wextra -Wpedantic -Wno-long-long -g -O2 -fno-strict-aliasing -MT cord/libcord_la-cordprnt.lo -MD -MP -MF cord/.deps/libcord_la-cordprnt.Tpo -c cord/cordprnt.c -fno-common -DPIC -o cord/libcord_la-cordprnt.o mv -f cord/.deps/libcord_la-cordprnt.Tpo cord/.deps/libcord_la-cordprnt.Plo /bin/sh ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -Wall -Wextra -Wpedantic -Wno-long-long -g -O2 -fno-strict-aliasing -MT cord/libcord_la-cordxtra.lo -MD -MP -MF cord/.deps/libcord_la-cordxtra.Tpo -c -o cord/libcord_la-cordxtra.lo `test -f 'cord/cordxtra.c' || echo './'`cord/cordxtra.c libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -Wall -Wextra -Wpedantic -Wno-long-long -g -O2 -fno-strict-aliasing -MT cord/libcord_la-cordxtra.lo -MD -MP -MF cord/.deps/libcord_la-cordxtra.Tpo -c cord/cordxtra.c -fno-common -DPIC -o cord/libcord_la-cordxtra.o mv -f cord/.deps/libcord_la-cordxtra.Tpo cord/.deps/libcord_la-cordxtra.Plo /bin/sh ./libtool --tag=CC --mode=link gcc -fexceptions -Wall -Wextra -Wpedantic -Wno-long-long -g -O2 -fno-strict-aliasing -version-info 6:0:5 -no-undefined -o libcord.la -rpath /usr/local/lib cord/libcord_la-cordbscs.lo cord/libcord_la-cordprnt.lo cord/libcord_la-cordxtra.lo libgc.la libtool: link: ar cru .libs/libcord.a cord/libcord_la-cordbscs.o cord/libcord_la-cordprnt.o cord/libcord_la-cordxtra.o libtool: link: ranlib .libs/libcord.a libtool: link: ( cd ".libs" && rm -f "libcord.la" && ln -s "../libcord.la" "libcord.la" ) cp .libs/libgc.a ../ cp .libs/libgccpp.a ../ ---------------------------------------- ------------------ GC ----------------- ---------------------------------------- --------- Compilation finished --------- ---------------------------------------- make --file=msaMakefile --directory=Muscle export PKG_CXXFLAGS=" -I../gc-8.2.2/include" /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB -o libMuscle.so aligngivenpath.cpp aligngivenpathsw.cpp aligntwomsas.cpp aligntwoprofs.cpp aln.cpp alpha.cpp anchors.cpp bittraceback.cpp blosum62.cpp blosumla.cpp clust.cpp cluster.cpp clwwt.cpp color.cpp cons.cpp diaglist.cpp diffobjscore.cpp diffpaths.cpp difftrees.cpp difftreese.cpp distcalc.cpp distfunc.cpp distpwkimura.cpp domuscle.cpp dosp.cpp dpreglist.cpp drawtree.cpp edgelist.cpp enumopts.cpp enumtostr.cpp estring.cpp fasta.cpp fasta2.cpp fastclust.cpp fastdist.cpp fastdistjones.cpp fastdistkbit.cpp fastdistkmer.cpp fastdistmafft.cpp fastdistnuc.cpp fastscorepath2.cpp finddiags.cpp finddiagsn.cpp glbalign.cpp glbalign352.cpp glbaligndiag.cpp glbalignle.cpp glbalignsimple.cpp glbalignsp.cpp glbalignspn.cpp glbalignss.cpp glbalndimer.cpp globals.cpp globalslinux.cpp globalsosx.cpp globalsother.cpp globalswin32.cpp gonnet.cpp henikoffweight.cpp henikoffweightpb.cpp html.cpp hydro.cpp intmath.cpp local.cpp main.cpp makerootmsa.cpp makerootmsab.cpp maketree.cpp mhack.cpp mpam200.cpp msa.cpp msa2.cpp msadistkimura.cpp msf.cpp muscle.cpp muscleout.cpp nucmx.cpp nwdasimple.cpp nwdasimple2.cpp nwdasmall.cpp nwrec.cpp nwsmall.cpp objscore.cpp objscore2.cpp objscoreda.cpp onexception.cpp options.cpp outweights.cpp pam200mafft.cpp params.cpp phy.cpp phy2.cpp phy3.cpp phy4.cpp phyfromclust.cpp phyfromfile.cpp physeq.cpp phytofile.cpp posgap.cpp ppscore.cpp profdb.cpp profile.cpp profilefrommsa.cpp progalign.cpp progress.cpp progressivealign.cpp pwpath.cpp readmx.cpp realigndiffs.cpp realigndiffse.cpp refine.cpp refinehoriz.cpp refinesubfams.cpp refinetree.cpp refinetreee.cpp refinevert.cpp refinew.cpp savebest.cpp scoredist.cpp scoregaps.cpp scorehistory.cpp scorepp.cpp seq.cpp seqvect.cpp setblosumweights.cpp setgscweights.cpp setnewhandler.cpp spfast.cpp sptest.cpp stabilize.cpp subfam.cpp subfams.cpp sw.cpp termgaps.cpp textfile.cpp threewaywt.cpp tomhydro.cpp traceback.cpp tracebackopt.cpp tracebacksw.cpp treefrommsa.cpp typetostr.cpp upgma2.cpp usage.cpp validateids.cpp vtml2.cpp writescorefile.cpp RMuscle.cpp using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c aligngivenpath.cpp -o aligngivenpath.o In file included from aligngivenpath.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ aligngivenpath.cpp:186:17: warning: unused variable 'uLengthA' [-Wunused-variable] const unsigned uLengthA = msaA.GetColCount(); ^ aligngivenpath.cpp:187:17: warning: unused variable 'uLengthB' [-Wunused-variable] const unsigned uLengthB = msaB.GetColCount(); ^ aligngivenpath.cpp:335:19: warning: unused variable 'uColA' [-Wunused-variable] const unsigned uColA = uPrefixLengthA - 1; ^ aligngivenpath.cpp:336:19: warning: unused variable 'uColB' [-Wunused-variable] const unsigned uColB = uPrefixLengthB - 1; ^ aligngivenpath.cpp:346:19: warning: unused variable 'uColA' [-Wunused-variable] const unsigned uColA = uPrefixLengthA - 1; ^ aligngivenpath.cpp:354:19: warning: unused variable 'uColB' [-Wunused-variable] const unsigned uColB = uPrefixLengthB - 1; ^ aligngivenpath.cpp:654:11: warning: variable 'uColIndexA' set but not used [-Wunused-but-set-variable] unsigned uColIndexA = 0; ^ aligngivenpath.cpp:655:11: warning: variable 'uColIndexB' set but not used [-Wunused-but-set-variable] unsigned uColIndexB = 0; ^ In file included from aligngivenpath.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 10 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c aligngivenpathsw.cpp -o aligngivenpathsw.o In file included from aligngivenpathsw.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ aligngivenpathsw.cpp:58:17: warning: unused variable 'uLengthA' [-Wunused-variable] const unsigned uLengthA = msaA.GetColCount(); ^ aligngivenpathsw.cpp:59:17: warning: unused variable 'uLengthB' [-Wunused-variable] const unsigned uLengthB = msaB.GetColCount(); ^ aligngivenpathsw.cpp:204:19: warning: unused variable 'uColA' [-Wunused-variable] const unsigned uColA = uPrefixLengthA - 1; ^ aligngivenpathsw.cpp:205:19: warning: unused variable 'uColB' [-Wunused-variable] const unsigned uColB = uPrefixLengthB - 1; ^ aligngivenpathsw.cpp:215:19: warning: unused variable 'uColA' [-Wunused-variable] const unsigned uColA = uPrefixLengthA - 1; ^ aligngivenpathsw.cpp:223:19: warning: unused variable 'uColB' [-Wunused-variable] const unsigned uColB = uPrefixLengthB - 1; ^ In file included from aligngivenpathsw.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 8 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c aligntwomsas.cpp -o aligntwomsas.o In file included from aligntwomsas.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from aligntwomsas.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c aligntwoprofs.cpp -o aligntwoprofs.o In file included from aligntwoprofs.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from aligntwoprofs.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c aln.cpp -o aln.o In file included from aln.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from aln.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c alpha.cpp -o alpha.o In file included from alpha.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ alpha.cpp:84:10: warning: enumeration value 'ALPHA_Undefined' not handled in switch [-Wswitch] switch (Alpha) ^~~~~ alpha.cpp:84:10: note: add missing switch cases switch (Alpha) ^ In file included from alpha.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c anchors.cpp -o anchors.o In file included from anchors.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ anchors.cpp:162:13: warning: unused variable 'uWindowCenter' [-Wunused-variable] unsigned uWindowCenter = uBestColIndex + uWindowLength/2; ^ In file included from anchors.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ anchors.cpp:53:13: warning: unused function 'FindBestColsGrade' [-Wunused-function] static void FindBestColsGrade(const SCORE Score[], unsigned uCount, ^ anchors.cpp:105:13: warning: unused function 'ListBestCols' [-Wunused-function] static void ListBestCols(const MSA &msa, const SCORE Score[], const SCORE SmoothScore[], ^ 5 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c bittraceback.cpp -o bittraceback.o In file included from bittraceback.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ bittraceback.cpp:146:7: warning: unused variable 'Bits' [-Wunused-variable] char Bits = TraceBack[uLengthA][uLengthB]; ^ In file included from bittraceback.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ bittraceback.cpp:15:20: warning: unused function 'BitsToStr' [-Wunused-function] static const char *BitsToStr(char Bits) ^ 4 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c blosum62.cpp -o blosum62.o In file included from blosum62.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from blosum62.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c blosumla.cpp -o blosumla.o In file included from blosumla.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from blosumla.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ blosumla.cpp:7:14: warning: unused variable 'Blosum62LA' [-Wunused-variable] static float Blosum62LA[20][20] = ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c clust.cpp -o clust.o In file included from clust.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ clust.cpp:167:10: warning: enumeration value 'JOIN_Undefined' not handled in switch [-Wswitch] switch (m_JoinStyle) ^~~~~~~~~~~ clust.cpp:167:10: note: add missing switch cases switch (m_JoinStyle) ^ clust.cpp:184:17: warning: unused variable 'uClusterCount' [-Wunused-variable] const unsigned uClusterCount = GetClusterCount(); ^ clust.cpp:204:17: warning: unused variable 'uClusterCount' [-Wunused-variable] const unsigned uClusterCount = GetClusterCount(); ^ clust.cpp:295:10: warning: enumeration value 'LINKAGE_Undefined' not handled in switch [-Wswitch] switch (m_CentroidStyle) ^~~~~~~~~~~~~~~ clust.cpp:295:10: note: add missing switch cases switch (m_CentroidStyle) ^ clust.cpp:360:14: warning: unused variable 'dDistLR' [-Wunused-variable] const float dDistLR = GetDist(uLeftNodeIndex, uRightNodeIndex); ^ clust.cpp:611:10: warning: enumeration value 'JOIN_Undefined' not handled in switch [-Wswitch] switch (m_JoinStyle) ^~~~~~~~~~~ clust.cpp:611:10: note: add missing switch cases switch (m_JoinStyle) ^ In file included from clust.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 8 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c cluster.cpp -o cluster.o In file included from cluster.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ cluster.cpp:284:8: warning: variable 'bFound' set but not used [-Wunused-but-set-variable] bool bFound = false; ^ cluster.cpp:267:9: warning: unused variable 'dMaxDist' [-Wunused-variable] double dMaxDist = 0.0; ^ In file included from cluster.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ cluster.cpp:10:21: warning: unused function 'Max' [-Wunused-function] static inline float Max(float d1, float d2) ^ cluster.cpp:15:21: warning: unused function 'Mean' [-Wunused-function] static inline float Mean(float d1, float d2) ^ 6 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c clwwt.cpp -o clwwt.o In file included from clwwt.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from clwwt.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c color.cpp -o color.o In file included from color.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ color.cpp:7:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] +4, -2, +0, -2, -1, -2, +0, -2, -1, -1, -1, -1, -2, -1, -1, -1, +1, +0, +0, -3, -1, -2, -1, // A ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } color.cpp:8:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] -2, +6, -3, +6, +2, -3, -1, -1, -3, -1, -4, -3, +1, -1, +0, -2, +0, -1, -3, -4, -1, -3, +2, // B ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } color.cpp:9:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] +0, -3, +9, -3, -4, -2, -3, -3, -1, -3, -1, -1, -3, -3, -3, -3, -1, -1, -1, -2, -1, -2, -4, // C ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } color.cpp:10:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] -2, +6, -3, +6, +2, -3, -1, -1, -3, -1, -4, -3, +1, -1, +0, -2, +0, -1, -3, -4, -1, -3, +2, // D ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } color.cpp:11:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] -1, +2, -4, +2, +5, -3, -2, +0, -3, +1, -3, -2, +0, -1, +2, +0, +0, -1, -2, -3, -1, -2, +5, // E ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } color.cpp:13:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] -2, -3, -2, -3, -3, +6, -3, -1, +0, -3, +0, +0, -3, -4, -3, -3, -2, -2, -1, +1, -1, +3, -3, // F ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } color.cpp:14:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] +0, -1, -3, -1, -2, -3, +6, -2, -4, -2, -4, -3, +0, -2, -2, -2, +0, -2, -3, -2, -1, -3, -2, // G ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } color.cpp:15:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] -2, -1, -3, -1, +0, -1, -2, +8, -3, -1, -3, -2, +1, -2, +0, +0, -1, -2, -3, -2, -1, +2, +0, // H ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } color.cpp:16:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] -1, -3, -1, -3, -3, +0, -4, -3, +4, -3, +2, +1, -3, -3, -3, -3, -2, -1, +3, -3, -1, -1, -3, // I ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } color.cpp:17:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] -1, -1, -3, -1, +1, -3, -2, -1, -3, +5, -2, -1, +0, -1, +1, +2, +0, -1, -2, -3, -1, -2, +1, // K ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } color.cpp:19:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] -1, -4, -1, -4, -3, +0, -4, -3, +2, -2, +4, +2, -3, -3, -2, -2, -2, -1, +1, -2, -1, -1, -3, // L ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } color.cpp:20:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] -1, -3, -1, -3, -2, +0, -3, -2, +1, -1, +2, +5, -2, -2, +0, -1, -1, -1, +1, -1, -1, -1, -2, // M ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } color.cpp:21:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] -2, +1, -3, +1, +0, -3, +0, +1, -3, +0, -3, -2, +6, -2, +0, +0, +1, +0, -3, -4, -1, -2, +0, // N ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } color.cpp:22:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] -1, -1, -3, -1, -1, -4, -2, -2, -3, -1, -3, -2, -2, +7, -1, -2, -1, -1, -2, -4, -1, -3, -1, // P ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } color.cpp:23:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] -1, +0, -3, +0, +2, -3, -2, +0, -3, +1, -2, +0, +0, -1, +5, +1, +0, -1, -2, -2, -1, -1, +2, // Q ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } color.cpp:25:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] -1, -2, -3, -2, +0, -3, -2, +0, -3, +2, -2, -1, +0, -2, +1, +5, -1, -1, -3, -3, -1, -2, +0, // R ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } color.cpp:26:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] +1, +0, -1, +0, +0, -2, +0, -1, -2, +0, -2, -1, +1, -1, +0, -1, +4, +1, -2, -3, -1, -2, +0, // S ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } color.cpp:27:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] +0, -1, -1, -1, -1, -2, -2, -2, -1, -1, -1, -1, +0, -1, -1, -1, +1, +5, +0, -2, -1, -2, -1, // T ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } color.cpp:28:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] +0, -3, -1, -3, -2, -1, -3, -3, +3, -2, +1, +1, -3, -2, -2, -3, -2, +0, +4, -3, -1, -1, -2, // V ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } color.cpp:29:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] -3, -4, -2, -4, -3, +1, -2, -2, -3, -3, -2, -1, -4, -4, -2, -3, -3, -2, -3,+11, -1, +2, -3, // W ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } color.cpp:31:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, // X ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } color.cpp:32:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] -2, -3, -2, -3, -2, +3, -3, +2, -1, -2, -1, -1, -2, -3, -1, -2, -2, -2, -1, +2, -1, +7, -2, // Y ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } color.cpp:33:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] -1, +2, -4, +2, +5, -3, -2, +0, -3, +1, -3, -2, +0, -1, +2, +0, +0, -1, -2, -3, -1, -2, +5, // Z ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } color.cpp:126:11: warning: variable 'uCharCount' set but not used [-Wunused-but-set-variable] unsigned uCharCount = 0; ^ In file included from color.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ color.cpp:72:12: warning: unused function 'BlosumScore' [-Wunused-function] static int BlosumScore(char c1, char c2) ^ 27 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c cons.cpp -o cons.o In file included from cons.cpp:7: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from cons.cpp:7: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c diaglist.cpp -o diaglist.o In file included from diaglist.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from diaglist.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c diffobjscore.cpp -o diffobjscore.o In file included from diffobjscore.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ diffobjscore.cpp:76:17: warning: unused variable 'uSeqCount' [-Wunused-variable] const unsigned uSeqCount = msa.GetSeqCount(); ^ diffobjscore.cpp:77:17: warning: unused variable 'uColCount' [-Wunused-variable] const unsigned uColCount = msa.GetColCount(); ^ In file included from diffobjscore.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 4 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c diffpaths.cpp -o diffpaths.o In file included from diffpaths.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from diffpaths.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c difftrees.cpp -o difftrees.o In file included from difftrees.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ difftrees.cpp:161:17: warning: unused variable 'uLeafCount2' [-Wunused-variable] const unsigned uLeafCount2 = Tree2.GetLeafCount(); ^ difftrees.cpp:296:11: warning: variable 'uDiffCount' set but not used [-Wunused-but-set-variable] unsigned uDiffCount = 0; ^ In file included from difftrees.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 4 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c difftreese.cpp -o difftreese.o In file included from difftreese.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from difftreese.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c distcalc.cpp -o distcalc.o In file included from distcalc.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from distcalc.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c distfunc.cpp -o distfunc.o In file included from distfunc.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from distfunc.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c distpwkimura.cpp -o distpwkimura.o In file included from distpwkimura.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from distpwkimura.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c domuscle.cpp -o domuscle.o In file included from domuscle.cpp:1: In file included from ./RMuscle.h:4: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ domuscle.cpp:180:6: warning: unused variable 'PNlength' [-Wunused-variable] int PNlength = (msaInput->inputSeqs).Length(); ^ In file included from domuscle.cpp:1: In file included from ./RMuscle.h:4: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c dosp.cpp -o dosp.o In file included from dosp.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from dosp.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c dpreglist.cpp -o dpreglist.o In file included from dpreglist.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ dpreglist.cpp:82:19: warning: unused variable 'uDiagLengthMinusCaps' [-Wunused-variable] const unsigned uDiagLengthMinusCaps = uEndVertexA - uStartVertexA - 1; ^ In file included from dpreglist.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c drawtree.cpp -o drawtree.o In file included from drawtree.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from drawtree.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c edgelist.cpp -o edgelist.o In file included from edgelist.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from edgelist.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c enumopts.cpp -o enumopts.o In file included from enumopts.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from enumopts.cpp:8: ./enums.h:12:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(ALPHA, Amino) ^~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :190:1: note: expanded from here "Amino" ^ In file included from enumopts.cpp:8: ./enums.h:13:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(ALPHA, DNA) ^~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :193:1: note: expanded from here "DNA" ^ In file included from enumopts.cpp:8: ./enums.h:14:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(ALPHA, RNA) ^~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :196:1: note: expanded from here "RNA" ^ In file included from enumopts.cpp:8: ./enums.h:15:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] e(ALPHA) ^~~~~~~~ { enumopts.cpp:6:15: note: expanded from macro 'e' #define e(t) 0, 0 }; ^~~~ In file included from enumopts.cpp:8: ./enums.h:18:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(SEQTYPE, Protein) ^~~~~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :200:1: note: expanded from here "Protein" ^ In file included from enumopts.cpp:8: ./enums.h:19:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(SEQTYPE, DNA) ^~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :203:1: note: expanded from here "DNA" ^ In file included from enumopts.cpp:8: ./enums.h:20:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(SEQTYPE, RNA) ^~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :206:1: note: expanded from here "RNA" ^ In file included from enumopts.cpp:8: ./enums.h:21:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(SEQTYPE, Auto) ^~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :209:1: note: expanded from here "Auto" ^ In file included from enumopts.cpp:8: ./enums.h:22:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] e(SEQTYPE) ^~~~~~~~~~ { enumopts.cpp:6:15: note: expanded from macro 'e' #define e(t) 0, 0 }; ^~~~ In file included from enumopts.cpp:8: ./enums.h:25:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(ROOT, Pseudo) ^~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :213:1: note: expanded from here "Pseudo" ^ In file included from enumopts.cpp:8: ./enums.h:26:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(ROOT, MidLongestSpan) ^~~~~~~~~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :216:1: note: expanded from here "MidLongestSpan" ^ In file included from enumopts.cpp:8: ./enums.h:27:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(ROOT, MinAvgLeafDist) ^~~~~~~~~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :219:1: note: expanded from here "MinAvgLeafDist" ^ In file included from enumopts.cpp:8: ./enums.h:28:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] e(ROOT) ^~~~~~~ { enumopts.cpp:6:15: note: expanded from macro 'e' #define e(t) 0, 0 }; ^~~~ In file included from enumopts.cpp:8: ./enums.h:31:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(CLUSTER, UPGMA) ^~~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :223:1: note: expanded from here "UPGMA" ^ In file included from enumopts.cpp:8: ./enums.h:32:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(CLUSTER, UPGMAMax) ^~~~~~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :226:1: note: expanded from here "UPGMAMax" ^ In file included from enumopts.cpp:8: ./enums.h:33:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(CLUSTER, UPGMAMin) ^~~~~~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :229:1: note: expanded from here "UPGMAMin" ^ In file included from enumopts.cpp:8: ./enums.h:34:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(CLUSTER, UPGMB) ^~~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :232:1: note: expanded from here "UPGMB" ^ In file included from enumopts.cpp:8: ./enums.h:35:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(CLUSTER, NeighborJoining) ^~~~~~~~~~~~~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :235:1: note: expanded from here "NeighborJoining" ^ In file included from enumopts.cpp:8: ./enums.h:36:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] e(CLUSTER) ^~~~~~~~~~ { enumopts.cpp:6:15: note: expanded from macro 'e' #define e(t) 0, 0 }; ^~~~ In file included from enumopts.cpp:8: ./enums.h:39:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(JOIN, NearestNeighbor) ^~~~~~~~~~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :239:1: note: expanded from here "NearestNeighbor" ^ In file included from enumopts.cpp:8: ./enums.h:40:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(JOIN, NeighborJoining) ^~~~~~~~~~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :242:1: note: expanded from here "NeighborJoining" ^ In file included from enumopts.cpp:8: ./enums.h:41:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] e(JOIN) ^~~~~~~ { enumopts.cpp:6:15: note: expanded from macro 'e' #define e(t) 0, 0 }; ^~~~ In file included from enumopts.cpp:8: ./enums.h:44:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(LINKAGE, Min) ^~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :246:1: note: expanded from here "Min" ^ In file included from enumopts.cpp:8: ./enums.h:45:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(LINKAGE, Avg) ^~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :249:1: note: expanded from here "Avg" ^ In file included from enumopts.cpp:8: ./enums.h:46:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(LINKAGE, Max) ^~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :252:1: note: expanded from here "Max" ^ In file included from enumopts.cpp:8: ./enums.h:47:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(LINKAGE, NeighborJoining) ^~~~~~~~~~~~~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :255:1: note: expanded from here "NeighborJoining" ^ In file included from enumopts.cpp:8: ./enums.h:48:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(LINKAGE, Biased) ^~~~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :258:1: note: expanded from here "Biased" ^ In file included from enumopts.cpp:8: ./enums.h:49:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] e(LINKAGE) ^~~~~~~~~~ { enumopts.cpp:6:15: note: expanded from macro 'e' #define e(t) 0, 0 }; ^~~~ In file included from enumopts.cpp:8: ./enums.h:52:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(DISTANCE, Kmer6_6) ^~~~~~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :262:1: note: expanded from here "Kmer6_6" ^ In file included from enumopts.cpp:8: ./enums.h:53:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(DISTANCE, Kmer20_3) ^~~~~~~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :265:1: note: expanded from here "Kmer20_3" ^ In file included from enumopts.cpp:8: ./enums.h:54:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(DISTANCE, Kmer20_4) ^~~~~~~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :268:1: note: expanded from here "Kmer20_4" ^ In file included from enumopts.cpp:8: ./enums.h:55:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(DISTANCE, Kbit20_3) ^~~~~~~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :271:1: note: expanded from here "Kbit20_3" ^ In file included from enumopts.cpp:8: ./enums.h:56:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(DISTANCE, Kmer4_6) ^~~~~~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :274:1: note: expanded from here "Kmer4_6" ^ In file included from enumopts.cpp:8: ./enums.h:57:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(DISTANCE, PctIdKimura) ^~~~~~~~~~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :277:1: note: expanded from here "PctIdKimura" ^ In file included from enumopts.cpp:8: ./enums.h:58:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(DISTANCE, PctIdLog) ^~~~~~~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :280:1: note: expanded from here "PctIdLog" ^ In file included from enumopts.cpp:8: ./enums.h:59:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(DISTANCE, PWKimura) ^~~~~~~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :283:1: note: expanded from here "PWKimura" ^ In file included from enumopts.cpp:8: ./enums.h:60:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(DISTANCE, PWScoreDist) ^~~~~~~~~~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :286:1: note: expanded from here "PWScoreDist" ^ In file included from enumopts.cpp:8: ./enums.h:61:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(DISTANCE, ScoreDist) ^~~~~~~~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :289:1: note: expanded from here "ScoreDist" ^ In file included from enumopts.cpp:8: ./enums.h:62:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(DISTANCE, Edit) ^~~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :292:1: note: expanded from here "Edit" ^ In file included from enumopts.cpp:8: ./enums.h:63:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] e(DISTANCE) ^~~~~~~~~~~ { enumopts.cpp:6:15: note: expanded from macro 'e' #define e(t) 0, 0 }; ^~~~ In file included from enumopts.cpp:8: ./enums.h:66:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(PPSCORE, LE) ^~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :296:1: note: expanded from here "LE" ^ In file included from enumopts.cpp:8: ./enums.h:67:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(PPSCORE, SP) ^~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :299:1: note: expanded from here "SP" ^ In file included from enumopts.cpp:8: ./enums.h:68:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(PPSCORE, SV) ^~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :302:1: note: expanded from here "SV" ^ In file included from enumopts.cpp:8: ./enums.h:69:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(PPSCORE, SPN) ^~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :305:1: note: expanded from here "SPN" ^ In file included from enumopts.cpp:8: ./enums.h:70:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] e(PPSCORE) ^~~~~~~~~~ { enumopts.cpp:6:15: note: expanded from macro 'e' #define e(t) 0, 0 }; ^~~~ In file included from enumopts.cpp:8: ./enums.h:73:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(SEQWEIGHT, None) ^~~~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :309:1: note: expanded from here "None" ^ In file included from enumopts.cpp:8: ./enums.h:74:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(SEQWEIGHT, Henikoff) ^~~~~~~~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :312:1: note: expanded from here "Henikoff" ^ In file included from enumopts.cpp:8: ./enums.h:75:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(SEQWEIGHT, HenikoffPB) ^~~~~~~~~~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :315:1: note: expanded from here "HenikoffPB" ^ In file included from enumopts.cpp:8: ./enums.h:76:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(SEQWEIGHT, GSC) ^~~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :318:1: note: expanded from here "GSC" ^ In file included from enumopts.cpp:8: ./enums.h:77:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(SEQWEIGHT, ClustalW) ^~~~~~~~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :321:1: note: expanded from here "ClustalW" ^ In file included from enumopts.cpp:8: ./enums.h:78:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(SEQWEIGHT, ThreeWay) ^~~~~~~~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :324:1: note: expanded from here "ThreeWay" ^ In file included from enumopts.cpp:8: ./enums.h:79:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] e(SEQWEIGHT) ^~~~~~~~~~~~ { enumopts.cpp:6:15: note: expanded from macro 'e' #define e(t) 0, 0 }; ^~~~ In file included from enumopts.cpp:8: ./enums.h:82:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(OBJSCORE, SP) // Sum of Pairs of sequences ^~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :328:1: note: expanded from here "SP" ^ In file included from enumopts.cpp:8: ./enums.h:83:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(OBJSCORE, DP) // Dynamic Programming score ^~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :3:1: note: expanded from here "DP" ^ In file included from enumopts.cpp:8: ./enums.h:84:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(OBJSCORE, XP) // Cross Pairs = sum of pairs between two MSAs ^~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :6:1: note: expanded from here "XP" ^ In file included from enumopts.cpp:8: ./enums.h:85:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(OBJSCORE, PS) // sum of Prof-Seq score for all seqs in MSA ^~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :9:1: note: expanded from here "PS" ^ In file included from enumopts.cpp:8: ./enums.h:86:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(OBJSCORE, SPF) // sum of pairs, fast approximation ^~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :12:1: note: expanded from here "SPF" ^ In file included from enumopts.cpp:8: ./enums.h:87:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(OBJSCORE, SPM) // sp if <= 100 seqs, spf otherwise ^~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :15:1: note: expanded from here "SPM" ^ In file included from enumopts.cpp:8: ./enums.h:88:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] e(OBJSCORE) ^~~~~~~~~~~ { enumopts.cpp:6:15: note: expanded from macro 'e' #define e(t) 0, 0 }; ^~~~ In file included from enumopts.cpp:8: ./enums.h:91:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(TERMGAPS, Full) ^~~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :19:1: note: expanded from here "Full" ^ In file included from enumopts.cpp:8: ./enums.h:92:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(TERMGAPS, Half) ^~~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :22:1: note: expanded from here "Half" ^ In file included from enumopts.cpp:8: ./enums.h:93:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] c(TERMGAPS, Ext) ^~~~~~~~~~~~~~~~ { enumopts.cpp:5:18: note: expanded from macro 'c' #define c(t, x) #x, t##_##x, ^~~~~~~~~~~ :25:1: note: expanded from here "Ext" ^ In file included from enumopts.cpp:8: ./enums.h:94:1: warning: suggest braces around initialization of subobject [-Wmissing-braces] e(TERMGAPS) ^~~~~~~~~~~ { enumopts.cpp:6:15: note: expanded from macro 'e' #define e(t) 0, 0 }; ^~~~ In file included from enumopts.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 65 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c enumtostr.cpp -o enumtostr.o In file included from enumtostr.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from enumtostr.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c estring.cpp -o estring.o In file included from estring.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ estring.cpp:397:8: warning: variable 'cType' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized] if (nB > 0) ^~~~~~ estring.cpp:409:11: note: uninitialized use occurs here switch (cType) ^~~~~ estring.cpp:397:4: note: remove the 'if' if its condition is always true if (nB > 0) ^~~~~~~~~~~ estring.cpp:395:12: warning: variable 'cType' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized] else if (nA < 0) ^~~~~~ estring.cpp:409:11: note: uninitialized use occurs here switch (cType) ^~~~~ estring.cpp:395:8: note: remove the 'if' if its condition is always true else if (nA < 0) ^~~~~~~~~~~ estring.cpp:386:13: warning: variable 'cType' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized] else if (nB < 0) ^~~~~~ estring.cpp:409:11: note: uninitialized use occurs here switch (cType) ^~~~~ estring.cpp:386:9: note: remove the 'if' if its condition is always true else if (nB < 0) ^~~~~~~~~~~ estring.cpp:377:13: note: initialize the variable 'cType' to silence this warning char cType; ^ = '\0' In file included from estring.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ estring.cpp:464:13: warning: unused function 'CanMultiplyEstrings' [-Wunused-function] static bool CanMultiplyEstrings(const short es1[], const short es2[]) ^ 6 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c fasta.cpp -o fasta.o In file included from fasta.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ fasta.cpp:15:11: warning: unused variable 'uSeqCount' [-Wunused-variable] unsigned uSeqCount = 0; ^ fasta.cpp:16:11: warning: unused variable 'uColCount' [-Wunused-variable] unsigned uColCount = uInsane; ^ In file included from fasta.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 4 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c fasta2.cpp -o fasta2.o In file included from fasta2.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from fasta2.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c fastclust.cpp -o fastclust.o In file included from fastclust.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from fastclust.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c fastdist.cpp -o fastdist.o In file included from fastdist.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from fastdist.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c fastdistjones.cpp -o fastdistjones.o In file included from fastdistjones.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from fastdistjones.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c fastdistkbit.cpp -o fastdistkbit.o In file included from fastdistkbit.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from fastdistkbit.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c fastdistkmer.cpp -o fastdistkmer.o In file included from fastdistkmer.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ fastdistkmer.cpp:235:11: warning: unused variable 'KD' [-Wunused-variable] double KD = KimuraDist(EstimatedPctId); ^ In file included from fastdistkmer.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c fastdistmafft.cpp -o fastdistmafft.o In file included from fastdistmafft.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ fastdistmafft.cpp:239:15: warning: unused variable 'pName1' [-Wunused-variable] const char *pName1 = s1.GetName(); ^ In file included from fastdistmafft.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ fastdistmafft.cpp:104:13: warning: unused function 'ListCount' [-Wunused-function] static void ListCount(const unsigned char Count[]) ^ 4 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c fastdistnuc.cpp -o fastdistnuc.o In file included from fastdistnuc.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ fastdistnuc.cpp:223:15: warning: unused variable 'pName1' [-Wunused-variable] const char *pName1 = s1.GetName(); ^ In file included from fastdistnuc.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ fastdistnuc.cpp:33:17: warning: unused variable 'uResidueGroupCount' [-Wunused-variable] static unsigned uResidueGroupCount = sizeof(ResidueGroup)/sizeof(ResidueGroup[0]); ^ fastdistnuc.cpp:85:13: warning: unused function 'ListCount' [-Wunused-function] static void ListCount(const unsigned char Count[]) ^ 5 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c fastscorepath2.cpp -o fastscorepath2.o In file included from fastscorepath2.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from fastscorepath2.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c finddiags.cpp -o finddiags.o In file included from finddiags.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from finddiags.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ finddiags.cpp:11:14: warning: unused function 'TupleToStr' [-Wunused-function] static char *TupleToStr(int t) ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c finddiagsn.cpp -o finddiagsn.o In file included from finddiagsn.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from finddiagsn.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ finddiagsn.cpp:12:14: warning: unused function 'TupleToStr' [-Wunused-function] static char *TupleToStr(int t) ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c glbalign.cpp -o glbalign.o In file included from glbalign.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from glbalign.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c glbalign352.cpp -o glbalign352.o In file included from glbalign352.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from glbalign352.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c glbaligndiag.cpp -o glbaligndiag.o In file included from glbaligndiag.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from glbaligndiag.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c glbalignle.cpp -o glbalignle.o In file included from glbalignle.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from glbalignle.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c glbalignsimple.cpp -o glbalignsimple.o In file included from glbalignsimple.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from glbalignsimple.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ glbalignsimple.cpp:28:13: warning: unused function 'ListTB' [-Wunused-function] static void ListTB(const char *TBM_, const ProfPos *PA, const ProfPos *PB, ^ glbalignsimple.cpp:52:13: warning: unused function 'ListDP' [-Wunused-function] static void ListDP(const SCORE *DPM_, const ProfPos *PA, const ProfPos *PB, ^ 4 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c glbalignsp.cpp -o glbalignsp.o In file included from glbalignsp.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from glbalignsp.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c glbalignspn.cpp -o glbalignspn.o In file included from glbalignspn.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from glbalignspn.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c glbalignss.cpp -o glbalignss.o In file included from glbalignss.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ glbalignss.cpp:177:16: warning: unused variable 'ptrRowA' [-Wunused-variable] const SCORE *ptrRowA = MxRowA[i]; ^ glbalignss.cpp:119:17: warning: unused variable 'uPrefixCountA' [-Wunused-variable] const unsigned uPrefixCountA = uLengthA + 1; ^ glbalignss.cpp:120:17: warning: unused variable 'uPrefixCountB' [-Wunused-variable] const unsigned uPrefixCountB = uLengthB + 1; ^ In file included from glbalignss.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ glbalignss.cpp:11:14: warning: unused function 'Subst' [-Wunused-function] static SCORE Subst(const Seq &seqA, const Seq &seqB, unsigned i, unsigned j) ^ 6 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c glbalndimer.cpp -o glbalndimer.o In file included from glbalndimer.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ glbalndimer.cpp:123:10: warning: enumeration values 'PPSCORE_Undefined' and 'PPSCORE_SPN' not handled in switch [-Wswitch] switch (g_PPScore) ^~~~~~~~~ glbalndimer.cpp:123:10: note: add missing switch cases switch (g_PPScore) ^ In file included from glbalndimer.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ glbalndimer.cpp:14:20: warning: unused function 'LocalScoreToStr' [-Wunused-function] static const char *LocalScoreToStr(SCORE s) ^ 4 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c globals.cpp -o globals.o In file included from globals.cpp:6: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from globals.cpp:6: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c globalslinux.cpp -o globalslinux.o In file included from globalslinux.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from globalslinux.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c globalsosx.cpp -o globalsosx.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c globalsother.cpp -o globalsother.o In file included from globalsother.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from globalsother.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c globalswin32.cpp -o globalswin32.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c gonnet.cpp -o gonnet.o In file included from gonnet.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from gonnet.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ gonnet.cpp:137:14: warning: unused variable 'Gonnet160' [-Wunused-variable] static SCORE Gonnet160[20][20] = ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c henikoffweight.cpp -o henikoffweight.o In file included from henikoffweight.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from henikoffweight.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c henikoffweightpb.cpp -o henikoffweightpb.o In file included from henikoffweightpb.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from henikoffweightpb.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c html.cpp -o html.o In file included from html.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from html.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c hydro.cpp -o hydro.o In file included from hydro.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from hydro.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c intmath.cpp -o intmath.o In file included from intmath.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ intmath.cpp:304:12: warning: variable 'uNumberGreater' set but not used [-Wunused-but-set-variable] unsigned uNumberGreater = 0; ^ intmath.cpp:328:12: warning: variable 'uNumberGreater' set but not used [-Wunused-but-set-variable] unsigned uNumberGreater = 0; ^ In file included from intmath.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 4 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c local.cpp -o local.o In file included from local.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from local.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c main.cpp -o main.o In file included from main.cpp:3: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from main.cpp:3: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c makerootmsa.cpp -o makerootmsa.o In file included from makerootmsa.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ makerootmsa.cpp:18:17: warning: unused variable 'uSeqLength' [-Wunused-variable] const unsigned uSeqLength = s.Length(); ^ makerootmsa.cpp:94:17: warning: unused variable 'Path' [-Wunused-variable] const PWPath &Path = Nodes[uNodeIndex].m_Path; ^ makerootmsa.cpp:168:17: warning: unused variable 'uTreeNodeCount' [-Wunused-variable] const unsigned uTreeNodeCount = GuideTree.GetNodeCount(); ^ In file included from makerootmsa.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ makerootmsa.cpp:12:13: warning: unused function 'PathSeq' [-Wunused-function] static void PathSeq(const Seq &s, const PWPath &Path, bool bRight, Seq &sOut) ^ 6 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c makerootmsab.cpp -o makerootmsab.o In file included from makerootmsab.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from makerootmsab.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c maketree.cpp -o maketree.o In file included from maketree.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from maketree.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c mhack.cpp -o mhack.o In file included from mhack.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from mhack.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c mpam200.cpp -o mpam200.o In file included from mpam200.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from mpam200.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c msa.cpp -o msa.o In file included from msa.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from msa.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ msa.cpp:385:13: warning: unused function 'FmtChar' [-Wunused-function] static void FmtChar(char c, unsigned uWidth) ^ msa.cpp:392:13: warning: unused function 'FmtInt' [-Wunused-function] static void FmtInt(unsigned u, unsigned uWidth) ^ msa.cpp:407:13: warning: unused function 'FmtInt0' [-Wunused-function] static void FmtInt0(unsigned u, unsigned uWidth) ^ msa.cpp:419:13: warning: unused function 'FmtPad' [-Wunused-function] static void FmtPad(unsigned n) ^ 6 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c msa2.cpp -o msa2.o In file included from msa2.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ msa2.cpp:357:10: warning: enumeration value 'SEQWEIGHT_Undefined' not handled in switch [-Wswitch] switch (Method) ^~~~~~ msa2.cpp:357:10: note: add missing switch cases switch (Method) ^ msa2.cpp:476:17: warning: unused variable 'uColCountCat' [-Wunused-variable] const unsigned uColCountCat = uColCount1 + uColCount2; ^ In file included from msa2.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 4 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c msadistkimura.cpp -o msadistkimura.o In file included from msadistkimura.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from msadistkimura.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c msf.cpp -o msf.o In file included from msf.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from msf.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ msf.cpp:24:20: warning: unused function 'strfind' [-Wunused-function] static const char *strfind(const char *s, const char *t) ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c muscle.cpp -o muscle.o In file included from muscle.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from muscle.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c muscleout.cpp -o muscleout.o In file included from muscleout.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from muscleout.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c nucmx.cpp -o nucmx.o In file included from nucmx.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from nucmx.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c nwdasimple.cpp -o nwdasimple.o In file included from nwdasimple.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from nwdasimple.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c nwdasimple2.cpp -o nwdasimple2.o In file included from nwdasimple2.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from nwdasimple2.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c nwdasmall.cpp -o nwdasmall.o In file included from nwdasmall.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from nwdasmall.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c nwrec.cpp -o nwrec.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c nwsmall.cpp -o nwsmall.o In file included from nwsmall.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ nwsmall.cpp:390:2: warning: variable 'Bit' is used uninitialized whenever switch default is taken [-Wsometimes-uninitialized] default: ^~~~~~~ nwsmall.cpp:394:14: note: uninitialized use occurs here TB[i][j] |= Bit; ^~~ nwsmall.cpp:378:10: note: initialize the variable 'Bit' to silence this warning char Bit; ^ = '\0' nwsmall.cpp:408:2: warning: variable 'Bit' is used uninitialized whenever switch default is taken [-Wsometimes-uninitialized] default: ^~~~~~~ nwsmall.cpp:412:14: note: uninitialized use occurs here TB[i][j] |= Bit; ^~~ nwsmall.cpp:399:10: note: initialize the variable 'Bit' to silence this warning char Bit; ^ = '\0' nwsmall.cpp:426:2: warning: variable 'Bit' is used uninitialized whenever switch default is taken [-Wsometimes-uninitialized] default: ^~~~~~~ nwsmall.cpp:430:14: note: uninitialized use occurs here TB[i][j] |= Bit; ^~~ nwsmall.cpp:417:10: note: initialize the variable 'Bit' to silence this warning char Bit; ^ = '\0' In file included from nwsmall.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ nwsmall.cpp:397:20: warning: unused function 'SetBitTBD' [-Wunused-function] static inline void SetBitTBD(char **TB, unsigned i, unsigned j, char c) ^ nwsmall.cpp:415:20: warning: unused function 'SetBitTBI' [-Wunused-function] static inline void SetBitTBI(char **TB, unsigned i, unsigned j, char c) ^ 7 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c objscore.cpp -o objscore.o In file included from objscore.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ objscore.cpp:31:10: warning: enumeration values 'OBJSCORE_Undefined' and 'OBJSCORE_SPM' not handled in switch [-Wswitch] switch (OS) ^~ objscore.cpp:31:10: note: add missing switch cases switch (OS) ^ In file included from objscore.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c objscore2.cpp -o objscore2.o In file included from objscore2.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ objscore2.cpp:22:10: warning: enumeration value 'TERMGAPS_Undefined' not handled in switch [-Wswitch] switch (g_TermGaps) ^~~~~~~~~~ objscore2.cpp:22:10: note: add missing switch cases switch (g_TermGaps) ^ objscore2.cpp:62:8: warning: unused variable 'scoreGaps' [-Wunused-variable] SCORE scoreGaps = 0; ^ objscore2.cpp:63:7: warning: unused variable 'bGapping1' [-Wunused-variable] bool bGapping1 = false; ^ objscore2.cpp:64:7: warning: unused variable 'bGapping2' [-Wunused-variable] bool bGapping2 = false; ^ objscore2.cpp:67:7: warning: variable 'bLeftTermGap' set but not used [-Wunused-but-set-variable] bool bLeftTermGap = false; ^ objscore2.cpp:82:7: warning: variable 'bRightTermGap' set but not used [-Wunused-but-set-variable] bool bRightTermGap = false; ^ objscore2.cpp:140:7: warning: variable 'bLeftTermGap' set but not used [-Wunused-but-set-variable] bool bLeftTermGap = false; ^ objscore2.cpp:155:7: warning: variable 'bRightTermGap' set but not used [-Wunused-but-set-variable] bool bRightTermGap = false; ^ objscore2.cpp:250:11: warning: variable 'uPairCount' set but not used [-Wunused-but-set-variable] unsigned uPairCount = 0; ^ objscore2.cpp:314:17: warning: unused variable 'uColCount2' [-Wunused-variable] const unsigned uColCount2 = msa2.GetColCount(); ^ objscore2.cpp:493:17: warning: unused variable 'w' [-Wunused-variable] const WEIGHT w = w1*w2; ^ In file included from objscore2.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 13 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c objscoreda.cpp -o objscoreda.o In file included from objscoreda.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from objscoreda.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c onexception.cpp -o onexception.o In file included from onexception.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from onexception.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c options.cpp -o options.o In file included from options.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ options.cpp:18:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "in", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:19:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "in1", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:20:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "in2", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:21:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "out", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:22:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "MaxIters", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:23:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "MaxHours", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:24:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "GapOpen", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:25:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "GapOpen2", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:26:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "GapExtend", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:27:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "GapExtend2", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:28:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "GapAmbig", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:29:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Center", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:30:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "SmoothScoreCeil", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:31:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "MinBestColScore", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:32:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "MinSmoothScore", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:33:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "ObjScore", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:34:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "SmoothWindow", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:35:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "RefineWindow", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:36:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "FromWindow", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:37:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "ToWindow", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:38:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "SaveWindow", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:39:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "WindowOffset", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:40:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "FirstWindow", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:41:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "AnchorSpacing", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:42:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Log", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:43:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "LogA", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:44:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "MaxTrees", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:45:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "SUEFF", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:46:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Distance", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:47:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Distance1", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:48:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Distance2", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:49:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Weight", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:50:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Weight1", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:51:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Weight2", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:52:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Cluster", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:53:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Cluster1", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:54:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Cluster2", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:55:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Root1", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:56:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Root2", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:57:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Tree1", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:58:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Tree2", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:59:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "UseTree", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:60:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "UseTree_NoWarn", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:61:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "DiagLength", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:62:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "DiagMargin", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:63:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "DiagBreak", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:64:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Hydro", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:65:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "HydroFactor", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:66:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "SPScore", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:67:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "SeqType", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:68:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "MaxMB", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:69:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "ComputeWeights", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:70:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "MaxSubFam", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:71:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "ScoreFile", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:72:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "TermGaps", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:73:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "FASTAOut", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:74:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "CLWOut", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:75:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "CLWStrictOut", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:76:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "HTMLOut", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:77:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "MSFOut", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:78:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "PHYIOut", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:79:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "PHYSOut", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:80:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Matrix", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:81:3: warning: suggest braces around initialization of subobject [-Wmissing-braces] "DistMx1", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:82:3: warning: suggest braces around initialization of subobject [-Wmissing-braces] "DistMx2", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:83:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Weight", 0, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:89:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "LE", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:90:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "SP", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:91:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "SV", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:92:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "SPN", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:93:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Core", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:94:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "NoCore", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:95:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Diags1", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:96:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Diags2", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:97:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Diags", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:98:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Quiet", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:99:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "MSF", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:100:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Verbose", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:101:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Anchors", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:102:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "NoAnchors", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:103:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Refine", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:104:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "RefineW", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:105:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "SW", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:106:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Profile", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:107:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "PPScore", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:108:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "ClusterOnly", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:109:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Brenner", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:110:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Dimer", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:111:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "clw", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:112:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "clwstrict", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:113:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "HTML", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:114:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Version", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:115:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Stable", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:116:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "Group", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:117:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "FASTA", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:118:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "ProfDB", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:119:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "PAS", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:120:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "PHYI", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:121:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "PHYS", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:122:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "TomHydro", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } options.cpp:123:2: warning: suggest braces around initialization of subobject [-Wmissing-braces] "MakeTree", false, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } In file included from options.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 103 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c outweights.cpp -o outweights.o In file included from outweights.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from outweights.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pam200mafft.cpp -o pam200mafft.o In file included from pam200mafft.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ pam200mafft.cpp:9:4: warning: suggest braces around initialization of subobject [-Wmissing-braces] 408, 20, 54, 52, -182, 179, -68, 109, -35, -47, 39, 106, 206, -14, -12, 257, 293, 191, -306, -219, 0, 0, 0, // A ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } pam200mafft.cpp:10:5: warning: suggest braces around initialization of subobject [-Wmissing-braces] 20, 1190, -228, -295, 94, 6, 63, -131, -184, -176, -112, -29, -122, -195, 49, 185, 13, -49, 199, 333, 0, 0, 0, // C ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } pam200mafft.cpp:11:5: warning: suggest braces around initialization of subobject [-Wmissing-braces] 54, -228, 645, 516, -399, 168, 98, -225, 75, -341, -235, 352, -149, 142, -44, 65, 7, -147, -418, -128, 0, 0, 0, // D ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } pam200mafft.cpp:12:5: warning: suggest braces around initialization of subobject [-Wmissing-braces] 52, -295, 516, 630, -460, 145, 45, -225, 195, -307, -222, 186, -121, 299, 54, -10, -36, -130, -366, -285, 0, 0, 0, // E ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } pam200mafft.cpp:13:3: warning: suggest braces around initialization of subobject [-Wmissing-braces] -182, 94, -399, -460, 908, -387, 82, 100, -423, 340, 87, -216, -160, -274, -307, -31, -153, 51, 19, 604, 0, 0, 0, // F ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } pam200mafft.cpp:14:4: warning: suggest braces around initialization of subobject [-Wmissing-braces] 179, 6, 168, 145, -387, 682, -94, -196, -14, -304, -226, 99, -57, -48, 117, 175, 41, -73, -38, -329, 0, 0, 0, // G ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } pam200mafft.cpp:15:4: warning: suggest braces around initialization of subobject [-Wmissing-braces] -68, 63, 98, 45, 82, -94, 786, -185, 164, -72, -132, 258, 86, 388, 277, 55, -15, -197, -181, 488, 0, 0, 0, // H ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } pam200mafft.cpp:16:4: warning: suggest braces around initialization of subobject [-Wmissing-braces] 109, -131, -225, -225, 100, -196, -185, 574, -204, 308, 411, -94, -95, -202, -188, 1, 182, 489, -254, -133, 0, 0, 0, // I ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } pam200mafft.cpp:17:4: warning: suggest braces around initialization of subobject [-Wmissing-braces] -35, -184, 75, 195, -423, -14, 164, -204, 652, -229, -98, 206, -66, 335, 486, 22, 39, -207, -196, -244, 0, 0, 0, // K ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } pam200mafft.cpp:18:4: warning: suggest braces around initialization of subobject [-Wmissing-braces] -47, -176, -341, -307, 340, -304, -72, 308, -229, 611, 389, -203, 73, -66, -150, -49, -21, 259, -46, -9, 0, 0, 0, // L ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } pam200mafft.cpp:19:5: warning: suggest braces around initialization of subobject [-Wmissing-braces] 39, -112, -235, -222, 87, -226, -132, 411, -98, 389, 776, -111, -78, -104, -109, -29, 149, 351, -209, -162, 0, 0, 0, // M ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } pam200mafft.cpp:20:4: warning: suggest braces around initialization of subobject [-Wmissing-braces] 106, -29, 352, 186, -216, 99, 258, -94, 206, -203, -111, 536, -1, 108, 93, 260, 188, -98, -359, 12, 0, 0, 0, // N ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } pam200mafft.cpp:21:4: warning: suggest braces around initialization of subobject [-Wmissing-braces] 206, -122, -149, -121, -160, -57, 86, -95, -66, 73, -78, -1, 756, 142, 25, 241, 159, -55, -353, -206, 0, 0, 0, // P ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } pam200mafft.cpp:22:4: warning: suggest braces around initialization of subobject [-Wmissing-braces] -14, -195, 142, 299, -274, -48, 388, -202, 335, -66, -104, 108, 142, 655, 321, 7, -15, -175, -223, -53, 0, 0, 0, // Q ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } pam200mafft.cpp:23:4: warning: suggest braces around initialization of subobject [-Wmissing-braces] -12, 49, -44, 54, -307, 117, 277, -188, 486, -150, -109, 93, 25, 321, 626, 48, 16, -181, 124, -113, 0, 0, 0, // R ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } pam200mafft.cpp:24:4: warning: suggest braces around initialization of subobject [-Wmissing-braces] 257, 185, 65, -10, -31, 175, 55, 1, 22, -49, -29, 260, 241, 7, 48, 373, 279, 28, -193, -35, 0, 0, 0, // S ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } pam200mafft.cpp:25:4: warning: suggest braces around initialization of subobject [-Wmissing-braces] 293, 13, 7, -36, -153, 41, -15, 182, 39, -21, 149, 188, 159, -15, 16, 279, 442, 163, -323, -170, 0, 0, 0, // T ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } pam200mafft.cpp:26:4: warning: suggest braces around initialization of subobject [-Wmissing-braces] 191, -49, -147, -130, 51, -73, -197, 489, -207, 259, 351, -98, -55, -175, -181, 28, 163, 525, -225, -177, 0, 0, 0, // V ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } pam200mafft.cpp:27:3: warning: suggest braces around initialization of subobject [-Wmissing-braces] -306, 199, -418, -366, 19, -38, -181, -254, -196, -46, -209, -359, -353, -223, 124, -193, -323, -225, 1495, 83, 0, 0, 0, // W ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } pam200mafft.cpp:28:3: warning: suggest braces around initialization of subobject [-Wmissing-braces] -219, 333, -128, -285, 604, -329, 488, -133, -244, -9, -162, 12, -206, -53, -113, -35, -170, -177, 83, 999, 0, 0, 0, // Y ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } pam200mafft.cpp:29:6: warning: suggest braces around initialization of subobject [-Wmissing-braces] 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, // B ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } pam200mafft.cpp:30:6: warning: suggest braces around initialization of subobject [-Wmissing-braces] 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, // Z ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } pam200mafft.cpp:31:6: warning: suggest braces around initialization of subobject [-Wmissing-braces] 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, // X ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } In file included from pam200mafft.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ pam200mafft.cpp:6:14: warning: unused variable 'PAM200' [-Wunused-variable] static float PAM200[23][23] = ^ 26 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c params.cpp -o params.o In file included from params.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ params.cpp:441:10: warning: enumeration value 'PPSCORE_Undefined' not handled in switch [-Wswitch] switch (g_PPScore) ^~~~~~~~~ params.cpp:441:10: note: add missing switch cases switch (g_PPScore) ^ In file included from params.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c phy.cpp -o phy.o In file included from phy.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ phy.cpp:665:9: warning: unused variable 'dEdgeLength' [-Wunused-variable] double dEdgeLength = GetEdgeLength(uNode1, uNode2); ^ In file included from phy.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c phy2.cpp -o phy2.o In file included from phy2.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from phy2.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c phy3.cpp -o phy3.o In file included from phy3.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ phy3.cpp:125:15: warning: unused variable 'dThisDist' [-Wunused-variable] const double dThisDist = tree.GetEdgeLength(uNode1, uNode2); ^ phy3.cpp:167:17: warning: unused variable 'uLeafCount' [-Wunused-variable] const unsigned uLeafCount = tree.GetLeafCount(); ^ phy3.cpp:190:9: warning: unused variable 'dAllMaxDist' [-Wunused-variable] double dAllMaxDist = -1e20; ^ phy3.cpp:191:11: warning: unused variable 'uMaxFrom' [-Wunused-variable] unsigned uMaxFrom = NULL_NEIGHBOR; ^ phy3.cpp:192:11: warning: unused variable 'uMaxTo' [-Wunused-variable] unsigned uMaxTo = NULL_NEIGHBOR; ^ phy3.cpp:263:11: warning: variable 'uMostDistantLeaf' set but not used [-Wunused-but-set-variable] unsigned uMostDistantLeaf = NULL_NEIGHBOR; ^ In file included from phy3.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ phy3.cpp:45:13: warning: unused function 'ListEIs' [-Wunused-function] static void ListEIs(EdgeInfo **EIs, unsigned uNodeCount) ^ 9 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c phy4.cpp -o phy4.o In file included from phy4.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from phy4.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c phyfromclust.cpp -o phyfromclust.o In file included from phyfromclust.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from phyfromclust.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c phyfromfile.cpp -o phyfromfile.o In file included from phyfromfile.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from phyfromfile.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c physeq.cpp -o physeq.o In file included from physeq.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from physeq.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c phytofile.cpp -o phytofile.o In file included from phytofile.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from phytofile.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c posgap.cpp -o posgap.o In file included from posgap.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from posgap.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ppscore.cpp -o ppscore.o In file included from ppscore.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from ppscore.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c profdb.cpp -o profdb.o In file included from profdb.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from profdb.cpp:9: In file included from ./clustsetmsa.h:8: ./msadist.h:22:10: warning: 10 enumeration values not handled in switch: 'DISTANCE_Undefined', 'DISTANCE_Kmer6_6', 'DISTANCE_Kmer20_3'... [-Wswitch] switch(m_Distance) ^~~~~~~~~~ ./msadist.h:22:10: note: add missing switch cases switch(m_Distance) ^ In file included from profdb.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c profile.cpp -o profile.o In file included from profile.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from profile.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c profilefrommsa.cpp -o profilefrommsa.o In file included from profilefrommsa.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ profilefrommsa.cpp:230:10: warning: enumeration value 'ALPHA_Undefined' not handled in switch [-Wswitch] switch (g_Alpha) ^~~~~~~ profilefrommsa.cpp:230:10: note: add missing switch cases switch (g_Alpha) ^ profilefrommsa.cpp:245:17: warning: unused variable 'uSeqCount' [-Wunused-variable] const unsigned uSeqCount = a.GetSeqCount(); ^ profilefrommsa.cpp:253:11: warning: unused variable 'uHydrophobicRunLength' [-Wunused-variable] unsigned uHydrophobicRunLength = 0; ^ In file included from profilefrommsa.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ profilefrommsa.cpp:15:20: warning: unused function 'LocalScoreToStr' [-Wunused-function] static const char *LocalScoreToStr(SCORE s) ^ 6 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c progalign.cpp -o progalign.o In file included from progalign.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ progalign.cpp:41:17: warning: unused variable 'uIterCount' [-Wunused-variable] const unsigned uIterCount = uSeqCount - 1; ^ In file included from progalign.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c progress.cpp -o progress.o In file included from progress.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from progress.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c progressivealign.cpp -o progressivealign.o In file included from progressivealign.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from progressivealign.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pwpath.cpp -o pwpath.o In file included from pwpath.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ pwpath.cpp:80:16: warning: unused variable 'LastEdge' [-Wunused-variable] const PWEdge &LastEdge = GetEdge(uEdgeCount - 1); ^ pwpath.cpp:81:11: warning: variable 'uStartA' set but not used [-Wunused-but-set-variable] unsigned uStartA = FirstEdge.uPrefixLengthA; ^ pwpath.cpp:82:11: warning: variable 'uStartB' set but not used [-Wunused-but-set-variable] unsigned uStartB = FirstEdge.uPrefixLengthB; ^ pwpath.cpp:213:11: warning: unused variable 'uEdgeIndex' [-Wunused-variable] unsigned uEdgeIndex = 0; ^ In file included from pwpath.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 6 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c readmx.cpp -o readmx.o In file included from readmx.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from readmx.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ readmx.cpp:30:17: warning: unused function 'MxCharToLetter' [-Wunused-function] static unsigned MxCharToLetter(char c) ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c realigndiffs.cpp -o realigndiffs.o In file included from realigndiffs.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from realigndiffs.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c realigndiffse.cpp -o realigndiffse.o In file included from realigndiffse.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ realigndiffse.cpp:77:13: warning: unused variable 'uNewRight' [-Wunused-variable] unsigned uNewRight = NewTree.GetRight(uNewNodeIndex); ^ realigndiffse.cpp:80:13: warning: unused variable 'uOldRight' [-Wunused-variable] unsigned uOldRight = OldTree.GetRight(uOld); ^ In file included from realigndiffse.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 4 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c refine.cpp -o refine.o In file included from refine.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from refine.cpp:9: In file included from ./clustsetmsa.h:8: ./msadist.h:22:10: warning: 10 enumeration values not handled in switch: 'DISTANCE_Undefined', 'DISTANCE_Kmer6_6', 'DISTANCE_Kmer20_3'... [-Wswitch] switch(m_Distance) ^~~~~~~~~~ ./msadist.h:22:10: note: add missing switch cases switch(m_Distance) ^ In file included from refine.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c refinehoriz.cpp -o refinehoriz.o In file included from refinehoriz.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ refinehoriz.cpp:260:4: warning: variable 'bRight' is used uninitialized whenever switch default is taken [-Wsometimes-uninitialized] default: ^~~~~~~ refinehoriz.cpp:263:56: note: uninitialized use occurs here RefineHeightParts(msaIn, tree, Internals, bReverse, bRight, ^~~~~~ refinehoriz.cpp:251:15: note: initialize the variable 'bRight' to silence this warning bool bRight; ^ = false In file included from refinehoriz.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c refinesubfams.cpp -o refinesubfams.o In file included from refinesubfams.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ refinesubfams.cpp:63:17: warning: unused variable 'uNodeCount' [-Wunused-variable] const unsigned uNodeCount = tree.GetNodeCount(); ^ In file included from refinesubfams.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c refinetree.cpp -o refinetree.o In file included from refinetree.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from refinetree.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c refinetreee.cpp -o refinetreee.o In file included from refinetreee.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from refinetreee.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c refinevert.cpp -o refinevert.o In file included from refinevert.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from refinevert.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c refinew.cpp -o refinew.o In file included from refinew.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ refinew.cpp:22:17: warning: unused variable 'uColCountCat' [-Wunused-variable] const unsigned uColCountCat = uColCount1 + uColCount2; ^ refinew.cpp:125:13: warning: unused variable 'uOutCols' [-Wunused-variable] unsigned uOutCols = msaOut.GetColCount(); ^ In file included from refinew.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 4 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c savebest.cpp -o savebest.o In file included from savebest.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from savebest.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c scoredist.cpp -o scoredist.o In file included from scoredist.cpp:3: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from scoredist.cpp:3: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ scoredist.cpp:17:21: warning: unused variable 'Dayhoff_CalibrationFactor' [-Wunused-const-variable] static const double Dayhoff_CalibrationFactor = 1.3370; ^ scoredist.cpp:19:21: warning: unused variable 'MV_CalibrationFactor' [-Wunused-const-variable] static const double MV_CalibrationFactor = 1.1775; ^ 4 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c scoregaps.cpp -o scoregaps.o In file included from scoregaps.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from scoregaps.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ scoregaps.cpp:37:13: warning: unused function 'FreeGapInfo' [-Wunused-function] static void FreeGapInfo(GAPINFO *GI) ^ scoregaps.cpp:80:14: warning: unused function 'Penalty' [-Wunused-function] static SCORE Penalty(unsigned Length, bool Term) ^ 4 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c scorehistory.cpp -o scorehistory.o In file included from scorehistory.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from scorehistory.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c scorepp.cpp -o scorepp.o In file included from scorepp.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from scorepp.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c seq.cpp -o seq.o In file included from seq.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from seq.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c seqvect.cpp -o seqvect.o In file included from seqvect.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ seqvect.cpp:201:17: warning: binding dereferenced null pointer to reference has undefined behavior [-Wnull-dereference] return (Seq &) *((Seq *) 0); ^~~~~~~~~~~~ In file included from seqvect.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ seqvect.cpp:6:14: warning: unused variable 'MAX_FASTA_LINE' [-Wunused-const-variable] const size_t MAX_FASTA_LINE = 16000; ^ 4 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c setblosumweights.cpp -o setblosumweights.o In file included from setblosumweights.cpp:42: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from setblosumweights.cpp:42: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c setgscweights.cpp -o setgscweights.o In file included from setgscweights.cpp:104: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from setgscweights.cpp:104: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c setnewhandler.cpp -o setnewhandler.o In file included from setnewhandler.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from setnewhandler.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c spfast.cpp -o spfast.o In file included from spfast.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ spfast.cpp:252:17: warning: unused variable 'uSeqCount' [-Wunused-variable] const unsigned uSeqCount = msa.GetSeqCount(); ^ In file included from spfast.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ spfast.cpp:14:20: warning: unused function 'GapTypeToStr' [-Wunused-function] static const char *GapTypeToStr(int GapType) ^ spfast.cpp:59:14: warning: unused function 'SPColBrute' [-Wunused-function] static SCORE SPColBrute(const MSA &msa, unsigned uColIndex) ^ 5 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c sptest.cpp -o sptest.o In file included from sptest.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from sptest.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c stabilize.cpp -o stabilize.o In file included from stabilize.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from stabilize.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c subfam.cpp -o subfam.o In file included from subfam.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ subfam.cpp:173:6: warning: unused variable 'NotUsed' [-Wunused-variable] int NotUsed = system(CmdLine); ^ In file included from subfam.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c subfams.cpp -o subfams.o In file included from subfams.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from subfams.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ subfams.cpp:12:13: warning: unused function 'GetMostDistantPair' [-Wunused-function] static void GetMostDistantPair(DistFunc &DF, unsigned *ptrIndex1, unsigned *ptrIndex2) ^ subfams.cpp:42:13: warning: unused function 'InitializeSingleSource' [-Wunused-function] static void InitializeSingleSource(DistFunc &DF, unsigned uIndex) ^ subfams.cpp:54:13: warning: unused function 'Relax' [-Wunused-function] static void Relax(DistFunc &DF, unsigned u, unsigned v) ^ 5 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c sw.cpp -o sw.o In file included from sw.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from sw.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ sw.cpp:20:13: warning: unused function 'ListDP' [-Wunused-function] static void ListDP(const SCORE *DPM_, const ProfPos *PA, const ProfPos *PB, ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c termgaps.cpp -o termgaps.o In file included from termgaps.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from termgaps.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c textfile.cpp -o textfile.o In file included from textfile.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ textfile.cpp:111:6: warning: unused variable 'i' [-Wunused-variable] int i = fputc(c, m_ptrFile); ^ textfile.cpp:124:6: warning: unused variable 'iError' [-Wunused-variable] int iError = fputs(szLine, m_ptrFile); ^ In file included from textfile.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 4 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c threewaywt.cpp -o threewaywt.o In file included from threewaywt.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from threewaywt.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c tomhydro.cpp -o tomhydro.o In file included from tomhydro.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from tomhydro.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c traceback.cpp -o traceback.o In file included from traceback.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ traceback.cpp:21:17: warning: unused variable 'uPrefixCountB' [-Wunused-variable] const unsigned uPrefixCountB = uLengthB + 1; ^ traceback.cpp:195:3: warning: variable 'cPrevEdgeType' is used uninitialized whenever switch default is taken [-Wsometimes-uninitialized] default: ^~~~~~~ traceback.cpp:202:15: note: uninitialized use occurs here cEdgeType = cPrevEdgeType; ^~~~~~~~~~~~~ traceback.cpp:186:13: warning: variable 'cPrevEdgeType' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized] else if (EQ(Score, scoreSI)) ^~~~~~~~~~~~~~~~~~ traceback.cpp:8:18: note: expanded from macro 'EQ' #define EQ(a, b) (fabs(a-b) < 0.1) ^~~~~~~~~~~~~~~~~ traceback.cpp:202:15: note: uninitialized use occurs here cEdgeType = cPrevEdgeType; ^~~~~~~~~~~~~ traceback.cpp:186:9: note: remove the 'if' if its condition is always true else if (EQ(Score, scoreSI)) ^~~~~~~~~~~~~~~~~~~~~~~ traceback.cpp:150:13: warning: variable 'cPrevEdgeType' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized] else if (EQ(Score, scoreSD)) ^~~~~~~~~~~~~~~~~~ traceback.cpp:8:18: note: expanded from macro 'EQ' #define EQ(a, b) (fabs(a-b) < 0.1) ^~~~~~~~~~~~~~~~~ traceback.cpp:202:15: note: uninitialized use occurs here cEdgeType = cPrevEdgeType; ^~~~~~~~~~~~~ traceback.cpp:150:9: note: remove the 'if' if its condition is always true else if (EQ(Score, scoreSD)) ^~~~~~~~~~~~~~~~~~~~~~~ traceback.cpp:112:13: warning: variable 'cPrevEdgeType' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized] else if (EQ(scoreSM, Score)) ^~~~~~~~~~~~~~~~~~ traceback.cpp:8:18: note: expanded from macro 'EQ' #define EQ(a, b) (fabs(a-b) < 0.1) ^~~~~~~~~~~~~~~~~ traceback.cpp:202:15: note: uninitialized use occurs here cEdgeType = cPrevEdgeType; ^~~~~~~~~~~~~ traceback.cpp:112:9: note: remove the 'if' if its condition is always true else if (EQ(scoreSM, Score)) ^~~~~~~~~~~~~~~~~~~~~~~ traceback.cpp:68:21: note: initialize the variable 'cPrevEdgeType' to silence this warning char cPrevEdgeType; ^ = '\0' In file included from traceback.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 7 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c tracebackopt.cpp -o tracebackopt.o In file included from tracebackopt.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from tracebackopt.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c tracebacksw.cpp -o tracebacksw.o In file included from tracebacksw.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ tracebacksw.cpp:22:17: warning: unused variable 'uPrefixCountB' [-Wunused-variable] const unsigned uPrefixCountB = uLengthB + 1; ^ tracebacksw.cpp:29:8: warning: unused variable 'scoreMax' [-Wunused-variable] SCORE scoreMax = DPM(uPrefixLengthA, uPrefixLengthB); ^ tracebacksw.cpp:175:3: warning: variable 'cPrevEdgeType' is used uninitialized whenever switch default is taken [-Wsometimes-uninitialized] default: ^~~~~~~ tracebacksw.cpp:182:15: note: uninitialized use occurs here cEdgeType = cPrevEdgeType; ^~~~~~~~~~~~~ tracebacksw.cpp:166:13: warning: variable 'cPrevEdgeType' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized] else if (EQ(Score, scoreSI)) ^~~~~~~~~~~~~~~~~~ tracebacksw.cpp:8:18: note: expanded from macro 'EQ' #define EQ(a, b) (fabs(a-b) < 0.1) ^~~~~~~~~~~~~~~~~ tracebacksw.cpp:182:15: note: uninitialized use occurs here cEdgeType = cPrevEdgeType; ^~~~~~~~~~~~~ tracebacksw.cpp:166:9: note: remove the 'if' if its condition is always true else if (EQ(Score, scoreSI)) ^~~~~~~~~~~~~~~~~~~~~~~ tracebacksw.cpp:130:13: warning: variable 'cPrevEdgeType' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized] else if (EQ(Score, scoreSD)) ^~~~~~~~~~~~~~~~~~ tracebacksw.cpp:8:18: note: expanded from macro 'EQ' #define EQ(a, b) (fabs(a-b) < 0.1) ^~~~~~~~~~~~~~~~~ tracebacksw.cpp:182:15: note: uninitialized use occurs here cEdgeType = cPrevEdgeType; ^~~~~~~~~~~~~ tracebacksw.cpp:130:9: note: remove the 'if' if its condition is always true else if (EQ(Score, scoreSD)) ^~~~~~~~~~~~~~~~~~~~~~~ tracebacksw.cpp:92:13: warning: variable 'cPrevEdgeType' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized] else if (EQ(scoreMatch, Score)) ^~~~~~~~~~~~~~~~~~~~~ tracebacksw.cpp:8:18: note: expanded from macro 'EQ' #define EQ(a, b) (fabs(a-b) < 0.1) ^~~~~~~~~~~~~~~~~ tracebacksw.cpp:182:15: note: uninitialized use occurs here cEdgeType = cPrevEdgeType; ^~~~~~~~~~~~~ tracebacksw.cpp:92:9: note: remove the 'if' if its condition is always true else if (EQ(scoreMatch, Score)) ^~~~~~~~~~~~~~~~~~~~~~~~~~ tracebacksw.cpp:43:21: note: initialize the variable 'cPrevEdgeType' to silence this warning char cPrevEdgeType; ^ = '\0' In file included from tracebacksw.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 8 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c treefrommsa.cpp -o treefrommsa.o In file included from treefrommsa.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from treefrommsa.cpp:5: In file included from ./clustsetmsa.h:8: ./msadist.h:22:10: warning: 10 enumeration values not handled in switch: 'DISTANCE_Undefined', 'DISTANCE_Kmer6_6', 'DISTANCE_Kmer20_3'... [-Wswitch] switch(m_Distance) ^~~~~~~~~~ ./msadist.h:22:10: note: add missing switch cases switch(m_Distance) ^ In file included from treefrommsa.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c typetostr.cpp -o typetostr.o In file included from typetostr.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from typetostr.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c upgma2.cpp -o upgma2.o In file included from upgma2.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ upgma2.cpp:272:4: warning: variable 'dtNewDist' is used uninitialized whenever switch default is taken [-Wsometimes-uninitialized] default: ^~~~~~~ upgma2.cpp:292:17: note: uninitialized use occurs here g_Dist[vL] = dtNewDist; ^~~~~~~~~ upgma2.cpp:252:20: note: initialize the variable 'dtNewDist' to silence this warning dist_t dtNewDist; ^ = 0.0 upgma2.cpp:366:4: warning: suggest braces around initialization of subobject [-Wmissing-braces] 0, 2, 14, 14, 20, ^~~~~~~~~~~~~~~~~ { } upgma2.cpp:367:4: warning: suggest braces around initialization of subobject [-Wmissing-braces] 2, 0, 14, 14, 20, ^~~~~~~~~~~~~~~~~ { } upgma2.cpp:368:4: warning: suggest braces around initialization of subobject [-Wmissing-braces] 14, 14, 0, 4, 20, ^~~~~~~~~~~~~~~~~~ { } upgma2.cpp:369:4: warning: suggest braces around initialization of subobject [-Wmissing-braces] 14, 14, 4, 0, 20, ^~~~~~~~~~~~~~~~~~ { } upgma2.cpp:370:4: warning: suggest braces around initialization of subobject [-Wmissing-braces] 20, 20, 20, 20, 0, ^~~~~~~~~~~~~~~~~~ { } In file included from upgma2.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ upgma2.cpp:68:13: warning: unused function 'ListState' [-Wunused-function] static void ListState() ^ 9 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c usage.cpp -o usage.o In file included from usage.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from usage.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c validateids.cpp -o validateids.o In file included from validateids.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from validateids.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c vtml2.cpp -o vtml2.o In file included from vtml2.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from vtml2.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c writescorefile.cpp -o writescorefile.o In file included from writescorefile.cpp:1: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ writescorefile.cpp:37:4: warning: variable 'Score' is used uninitialized whenever switch default is taken [-Wsometimes-uninitialized] default: ^~~~~~~ writescorefile.cpp:40:12: note: uninitialized use occurs here dSum += Score; ^~~~~ writescorefile.cpp:27:16: note: initialize the variable 'Score' to silence this warning double Score; ^ = 0.0 In file included from writescorefile.cpp:1: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RMuscle.cpp -o RMuscle.o In file included from RMuscle.cpp:1: In file included from ./RMuscle.h:4: ./muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined] #define assert(exp) ((void)0) ^ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/assert.h:56:9: note: previous definition is here #define assert(e) ((void)0) ^ In file included from RMuscle.cpp:1: In file included from ./RMuscle.h:4: In file included from ./muscle.h:38: ./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. 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 libMuscle.so aligngivenpath.o aligngivenpathsw.o aligntwomsas.o aligntwoprofs.o aln.o alpha.o anchors.o bittraceback.o blosum62.o blosumla.o clust.o cluster.o clwwt.o color.o cons.o diaglist.o diffobjscore.o diffpaths.o difftrees.o difftreese.o distcalc.o distfunc.o distpwkimura.o domuscle.o dosp.o dpreglist.o drawtree.o edgelist.o enumopts.o enumtostr.o estring.o fasta.o fasta2.o fastclust.o fastdist.o fastdistjones.o fastdistkbit.o fastdistkmer.o fastdistmafft.o fastdistnuc.o fastscorepath2.o finddiags.o finddiagsn.o glbalign.o glbalign352.o glbaligndiag.o glbalignle.o glbalignsimple.o glbalignsp.o glbalignspn.o glbalignss.o glbalndimer.o globals.o globalslinux.o globalsosx.o globalsother.o globalswin32.o gonnet.o henikoffweight.o henikoffweightpb.o html.o hydro.o intmath.o local.o main.o makerootmsa.o makerootmsab.o maketree.o mhack.o mpam200.o msa.o msa2.o msadistkimura.o msf.o muscle.o muscleout.o nucmx.o nwdasimple.o nwdasimple2.o nwdasmall.o nwrec.o nwsmall.o objscore.o objscore2.o objscoreda.o onexception.o options.o outweights.o pam200mafft.o params.o phy.o phy2.o phy3.o phy4.o phyfromclust.o phyfromfile.o physeq.o phytofile.o posgap.o ppscore.o profdb.o profile.o profilefrommsa.o progalign.o progress.o progressivealign.o pwpath.o readmx.o realigndiffs.o realigndiffse.o refine.o refinehoriz.o refinesubfams.o refinetree.o refinetreee.o refinevert.o refinew.o savebest.o scoredist.o scoregaps.o scorehistory.o scorepp.o seq.o seqvect.o setblosumweights.o setgscweights.o setnewhandler.o spfast.o sptest.o stabilize.o subfam.o subfams.o sw.o termgaps.o textfile.o threewaywt.o tomhydro.o traceback.o tracebackopt.o tracebacksw.o treefrommsa.o typetostr.o upgma2.o usage.o validateids.o vtml2.o writescorefile.o RMuscle.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation ar rcs libMuscle.a aligngivenpath.o aligngivenpathsw.o aligntwomsas.o aligntwoprofs.o aln.o alpha.o anchors.o bittraceback.o blosum62.o blosumla.o clust.o cluster.o clwwt.o color.o cons.o diaglist.o diffobjscore.o diffpaths.o difftrees.o difftreese.o distcalc.o distfunc.o distpwkimura.o domuscle.o dosp.o dpreglist.o drawtree.o edgelist.o enumopts.o enumtostr.o estring.o fasta.o fasta2.o fastclust.o fastdist.o fastdistjones.o fastdistkbit.o fastdistkmer.o fastdistmafft.o fastdistnuc.o fastscorepath2.o finddiags.o finddiagsn.o glbalign.o glbalign352.o glbaligndiag.o glbalignle.o glbalignsimple.o glbalignsp.o glbalignspn.o glbalignss.o glbalndimer.o globals.o globalslinux.o globalsosx.o globalsother.o globalswin32.o gonnet.o henikoffweight.o henikoffweightpb.o html.o hydro.o intmath.o local.o main.o makerootmsa.o makerootmsab.o maketree.o mhack.o mpam200.o msa.o msa2.o msadistkimura.o msf.o muscle.o muscleout.o nucmx.o nwdasimple.o nwdasimple2.o nwdasmall.o nwrec.o nwsmall.o objscore.o objscore2.o objscoreda.o onexception.o options.o outweights.o pam200mafft.o params.o phy.o phy2.o phy3.o phy4.o phyfromclust.o phyfromfile.o physeq.o phytofile.o posgap.o ppscore.o profdb.o profile.o profilefrommsa.o progalign.o progress.o progressivealign.o pwpath.o readmx.o realigndiffs.o realigndiffse.o refine.o refinehoriz.o refinesubfams.o refinetree.o refinetreee.o refinevert.o refinew.o savebest.o scoredist.o scoregaps.o scorehistory.o scorepp.o seq.o seqvect.o setblosumweights.o setgscweights.o setnewhandler.o spfast.o sptest.o stabilize.o subfam.o subfams.o sw.o termgaps.o textfile.o threewaywt.o tomhydro.o traceback.o tracebackopt.o tracebacksw.o treefrommsa.o typetostr.o upgma2.o usage.o validateids.o vtml2.o writescorefile.o RMuscle.o cp libMuscle.a ../ ---------------------------------------- ---------------- MUSCLE ---------------- ---------------------------------------- --------- Compilation finished --------- ---------------------------------------- make --file=msaMakefile --directory=ClustalW ./configure; \ cd src; \ export PKG_CXXFLAGS="-DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result"; \ /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB -o libClustalW.so pairwise/FullPairwiseAlign.cpp pairwise/FastPairwiseAlign.cpp fileInput/MSFFileParser.cpp fileInput/FileReader.cpp fileInput/PIRFileParser.cpp fileInput/RSFFileParser.cpp fileInput/GDEFileParser.cpp fileInput/InFileStream.cpp fileInput/ClustalFileParser.cpp fileInput/PearsonFileParser.cpp fileInput/FileParser.cpp fileInput/EMBLFileParser.cpp tree/UPGMA/RootedClusterTree.cpp tree/UPGMA/UPGMAAlgorithm.cpp tree/UPGMA/Node.cpp tree/UPGMA/RootedGuideTree.cpp tree/UPGMA/RootedTreeOutput.cpp tree/Tree.cpp tree/ClusterTree.cpp tree/TreeInterface.cpp tree/UnRootedClusterTree.cpp tree/ClusterTreeOutput.cpp tree/RandomGenerator.cpp tree/NJTree.cpp tree/AlignmentSteps.cpp interface/CommandLineParser.cpp substitutionMatrix/SubMatrix.cpp multipleAlign/Iteration.cpp multipleAlign/MSA.cpp multipleAlign/MyersMillerProfileAlign.cpp multipleAlign/ProfileStandard.cpp multipleAlign/ProfileWithSub.cpp multipleAlign/ProfileBase.cpp multipleAlign/LowScoreSegProfile.cpp general/OutputFile.cpp general/UserParameters.cpp general/Utility.cpp general/InvalidCombination.cpp general/DebugLog.cpp general/ClustalWResources.cpp general/VectorOutOfRange.cpp general/SymMatrix.cpp general/Stats.cpp Help.cpp alignment/Alignment.cpp alignment/AlignmentOutput.cpp alignment/ObjectiveScore.cpp alignment/Sequence.cpp Clustal.cpp RClustalWMain.cpp RClustalW.cpp && \ ar rcs libClustalW.a pairwise/FullPairwiseAlign.o pairwise/FastPairwiseAlign.o fileInput/MSFFileParser.o fileInput/FileReader.o fileInput/PIRFileParser.o fileInput/RSFFileParser.o fileInput/GDEFileParser.o fileInput/InFileStream.o fileInput/ClustalFileParser.o fileInput/PearsonFileParser.o fileInput/FileParser.o fileInput/EMBLFileParser.o tree/UPGMA/RootedClusterTree.o tree/UPGMA/UPGMAAlgorithm.o tree/UPGMA/Node.o tree/UPGMA/RootedGuideTree.o tree/UPGMA/RootedTreeOutput.o tree/Tree.o tree/ClusterTree.o tree/TreeInterface.o tree/UnRootedClusterTree.o tree/ClusterTreeOutput.o tree/RandomGenerator.o tree/NJTree.o tree/AlignmentSteps.o interface/CommandLineParser.o substitutionMatrix/SubMatrix.o multipleAlign/Iteration.o multipleAlign/MSA.o multipleAlign/MyersMillerProfileAlign.o multipleAlign/ProfileStandard.o multipleAlign/ProfileWithSub.o multipleAlign/ProfileBase.o multipleAlign/LowScoreSegProfile.o general/OutputFile.o general/UserParameters.o general/Utility.o general/InvalidCombination.o general/DebugLog.o general/ClustalWResources.o general/VectorOutOfRange.o general/SymMatrix.o general/Stats.o Help.o alignment/Alignment.o alignment/AlignmentOutput.o alignment/ObjectiveScore.o alignment/Sequence.o Clustal.o RClustalWMain.o RClustalW.o && \ cp libClustalW.a ../../ checking build system type... aarch64-apple-darwin22.6.0 checking host system type... aarch64-apple-darwin22.6.0 checking target system type... aarch64-apple-darwin22.6.0 building for darwin22.6.0 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 sets $(MAKE)... (cached) yes 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 for style of include used by make... GNU 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 for ranlib... ranlib checking how to run the C++ preprocessor... g++ -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 stdbool.h that conforms to C99... no checking for _Bool... no checking for an ANSI C-conforming const... yes checking for size_t... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... yes configure: creating ./config.status config.status: creating Makefile config.status: creating m4/Makefile config.status: creating src/Makefile config.status: creating src/clustalw_version.h config.status: creating src/config.h config.status: executing depfiles commands using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -falign-functions=64 -Wall -g -O2 -c pairwise/FullPairwiseAlign.cpp -o pairwise/FullPairwiseAlign.o In file included from pairwise/FullPairwiseAlign.cpp:9: In file included from pairwise/FullPairwiseAlign.h:9: In file included from pairwise/PairwiseAlignBase.h:10: In file included from pairwise/../alignment/Alignment.h:41: In file included from pairwise/../alignment/Sequence.h:20: In file included from pairwise/../alignment/../general/userparams.h:8: In file included from pairwise/../alignment/../general/UserParameters.h:22: In file included from pairwise/../alignment/../general/utils.h:8: In file included from pairwise/../alignment/../general/Utility.h:15: In file included from pairwise/../alignment/../general/clustalw.h:42: pairwise/../alignment/../general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from pairwise/FullPairwiseAlign.cpp:9: In file included from pairwise/FullPairwiseAlign.h:9: In file included from pairwise/PairwiseAlignBase.h:10: In file included from pairwise/../alignment/Alignment.h:41: In file included from pairwise/../alignment/Sequence.h:20: In file included from pairwise/../alignment/../general/userparams.h:8: In file included from pairwise/../alignment/../general/UserParameters.h:22: In file included from pairwise/../alignment/../general/utils.h:8: In file included from pairwise/../alignment/../general/Utility.h:15: In file included from pairwise/../alignment/../general/clustalw.h:43: pairwise/../alignment/../general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ pairwise/FullPairwiseAlign.cpp:229:15: warning: variable 'pos' set but not used [-Wunused-but-set-variable] int i, k, pos, toDo; ^ In file included from pairwise/FullPairwiseAlign.cpp:9: In file included from pairwise/FullPairwiseAlign.h:9: In file included from pairwise/PairwiseAlignBase.h:10: In file included from pairwise/../alignment/Alignment.h:41: In file included from pairwise/../alignment/Sequence.h:20: In file included from pairwise/../alignment/../general/userparams.h:8: In file included from pairwise/../alignment/../general/UserParameters.h:22: In file included from pairwise/../alignment/../general/utils.h:8: In file included from pairwise/../alignment/../general/Utility.h:15: In file included from pairwise/../alignment/../general/clustalw.h:44: pairwise/../alignment/../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 4 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -falign-functions=64 -Wall -g -O2 -c pairwise/FastPairwiseAlign.cpp -o pairwise/FastPairwiseAlign.o In file included from pairwise/FastPairwiseAlign.cpp:10: In file included from pairwise/FastPairwiseAlign.h:9: In file included from pairwise/PairwiseAlignBase.h:10: In file included from pairwise/../alignment/Alignment.h:41: In file included from pairwise/../alignment/Sequence.h:20: In file included from pairwise/../alignment/../general/userparams.h:8: In file included from pairwise/../alignment/../general/UserParameters.h:22: In file included from pairwise/../alignment/../general/utils.h:8: In file included from pairwise/../alignment/../general/Utility.h:15: In file included from pairwise/../alignment/../general/clustalw.h:42: pairwise/../alignment/../general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from pairwise/FastPairwiseAlign.cpp:10: In file included from pairwise/FastPairwiseAlign.h:9: In file included from pairwise/PairwiseAlignBase.h:10: In file included from pairwise/../alignment/Alignment.h:41: In file included from pairwise/../alignment/Sequence.h:20: In file included from pairwise/../alignment/../general/userparams.h:8: In file included from pairwise/../alignment/../general/UserParameters.h:22: In file included from pairwise/../alignment/../general/utils.h:8: In file included from pairwise/../alignment/../general/Utility.h:15: In file included from pairwise/../alignment/../general/clustalw.h:43: pairwise/../alignment/../general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from pairwise/FastPairwiseAlign.cpp:10: In file included from pairwise/FastPairwiseAlign.h:9: In file included from pairwise/PairwiseAlignBase.h:10: In file included from pairwise/../alignment/Alignment.h:41: In file included from pairwise/../alignment/Sequence.h:20: In file included from pairwise/../alignment/../general/userparams.h:8: In file included from pairwise/../alignment/../general/UserParameters.h:22: In file included from pairwise/../alignment/../general/utils.h:8: In file included from pairwise/../alignment/../general/Utility.h:15: In file included from pairwise/../alignment/../general/clustalw.h:44: pairwise/../alignment/../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -falign-functions=64 -Wall -g -O2 -c fileInput/MSFFileParser.cpp -o fileInput/MSFFileParser.o In file included from fileInput/MSFFileParser.cpp:16: In file included from fileInput/MSFFileParser.h:10: In file included from fileInput/FileParser.h:22: In file included from fileInput/../alignment/Sequence.h:20: In file included from fileInput/../alignment/../general/userparams.h:8: In file included from fileInput/../alignment/../general/UserParameters.h:22: In file included from fileInput/../alignment/../general/utils.h:8: In file included from fileInput/../alignment/../general/Utility.h:15: In file included from fileInput/../alignment/../general/clustalw.h:42: fileInput/../alignment/../general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from fileInput/MSFFileParser.cpp:16: In file included from fileInput/MSFFileParser.h:10: In file included from fileInput/FileParser.h:22: In file included from fileInput/../alignment/Sequence.h:20: In file included from fileInput/../alignment/../general/userparams.h:8: In file included from fileInput/../alignment/../general/UserParameters.h:22: In file included from fileInput/../alignment/../general/utils.h:8: In file included from fileInput/../alignment/../general/Utility.h:15: In file included from fileInput/../alignment/../general/clustalw.h:43: fileInput/../alignment/../general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from fileInput/MSFFileParser.cpp:16: In file included from fileInput/MSFFileParser.h:10: In file included from fileInput/FileParser.h:22: In file included from fileInput/../alignment/Sequence.h:20: In file included from fileInput/../alignment/../general/userparams.h:8: In file included from fileInput/../alignment/../general/UserParameters.h:22: In file included from fileInput/../alignment/../general/utils.h:8: In file included from fileInput/../alignment/../general/Utility.h:15: In file included from fileInput/../alignment/../general/clustalw.h:44: fileInput/../alignment/../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -falign-functions=64 -Wall -g -O2 -c fileInput/FileReader.cpp -o fileInput/FileReader.o In file included from fileInput/FileReader.cpp:29: In file included from fileInput/FileReader.h:12: In file included from fileInput/../alignment/Alignment.h:41: In file included from fileInput/../alignment/Sequence.h:20: In file included from fileInput/../alignment/../general/userparams.h:8: In file included from fileInput/../alignment/../general/UserParameters.h:22: In file included from fileInput/../alignment/../general/utils.h:8: In file included from fileInput/../alignment/../general/Utility.h:15: In file included from fileInput/../alignment/../general/clustalw.h:42: fileInput/../alignment/../general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from fileInput/FileReader.cpp:29: In file included from fileInput/FileReader.h:12: In file included from fileInput/../alignment/Alignment.h:41: In file included from fileInput/../alignment/Sequence.h:20: In file included from fileInput/../alignment/../general/userparams.h:8: In file included from fileInput/../alignment/../general/UserParameters.h:22: In file included from fileInput/../alignment/../general/utils.h:8: In file included from fileInput/../alignment/../general/Utility.h:15: In file included from fileInput/../alignment/../general/clustalw.h:43: fileInput/../alignment/../general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ fileInput/FileReader.cpp:421:10: warning: variable 'maxAlnLength' set but not used [-Wunused-but-set-variable] int maxAlnLength; // Get values from the Alignment object. ^ In file included from fileInput/FileReader.cpp:29: In file included from fileInput/FileReader.h:12: In file included from fileInput/../alignment/Alignment.h:41: In file included from fileInput/../alignment/Sequence.h:20: In file included from fileInput/../alignment/../general/userparams.h:8: In file included from fileInput/../alignment/../general/UserParameters.h:22: In file included from fileInput/../alignment/../general/utils.h:8: In file included from fileInput/../alignment/../general/Utility.h:15: In file included from fileInput/../alignment/../general/clustalw.h:44: fileInput/../alignment/../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 4 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -falign-functions=64 -Wall -g -O2 -c fileInput/PIRFileParser.cpp -o fileInput/PIRFileParser.o In file included from fileInput/PIRFileParser.cpp:16: In file included from fileInput/PIRFileParser.h:10: In file included from fileInput/FileParser.h:22: In file included from fileInput/../alignment/Sequence.h:20: In file included from fileInput/../alignment/../general/userparams.h:8: In file included from fileInput/../alignment/../general/UserParameters.h:22: In file included from fileInput/../alignment/../general/utils.h:8: In file included from fileInput/../alignment/../general/Utility.h:15: In file included from fileInput/../alignment/../general/clustalw.h:42: fileInput/../alignment/../general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from fileInput/PIRFileParser.cpp:16: In file included from fileInput/PIRFileParser.h:10: In file included from fileInput/FileParser.h:22: In file included from fileInput/../alignment/Sequence.h:20: In file included from fileInput/../alignment/../general/userparams.h:8: In file included from fileInput/../alignment/../general/UserParameters.h:22: In file included from fileInput/../alignment/../general/utils.h:8: In file included from fileInput/../alignment/../general/Utility.h:15: In file included from fileInput/../alignment/../general/clustalw.h:43: fileInput/../alignment/../general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from fileInput/PIRFileParser.cpp:16: In file included from fileInput/PIRFileParser.h:10: In file included from fileInput/FileParser.h:22: In file included from fileInput/../alignment/Sequence.h:20: In file included from fileInput/../alignment/../general/userparams.h:8: In file included from fileInput/../alignment/../general/UserParameters.h:22: In file included from fileInput/../alignment/../general/utils.h:8: In file included from fileInput/../alignment/../general/Utility.h:15: In file included from fileInput/../alignment/../general/clustalw.h:44: fileInput/../alignment/../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -falign-functions=64 -Wall -g -O2 -c fileInput/RSFFileParser.cpp -o fileInput/RSFFileParser.o In file included from fileInput/RSFFileParser.cpp:16: In file included from fileInput/RSFFileParser.h:10: In file included from fileInput/FileParser.h:22: In file included from fileInput/../alignment/Sequence.h:20: In file included from fileInput/../alignment/../general/userparams.h:8: In file included from fileInput/../alignment/../general/UserParameters.h:22: In file included from fileInput/../alignment/../general/utils.h:8: In file included from fileInput/../alignment/../general/Utility.h:15: In file included from fileInput/../alignment/../general/clustalw.h:42: fileInput/../alignment/../general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from fileInput/RSFFileParser.cpp:16: In file included from fileInput/RSFFileParser.h:10: In file included from fileInput/FileParser.h:22: In file included from fileInput/../alignment/Sequence.h:20: In file included from fileInput/../alignment/../general/userparams.h:8: In file included from fileInput/../alignment/../general/UserParameters.h:22: In file included from fileInput/../alignment/../general/utils.h:8: In file included from fileInput/../alignment/../general/Utility.h:15: In file included from fileInput/../alignment/../general/clustalw.h:43: fileInput/../alignment/../general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from fileInput/RSFFileParser.cpp:16: In file included from fileInput/RSFFileParser.h:10: In file included from fileInput/FileParser.h:22: In file included from fileInput/../alignment/Sequence.h:20: In file included from fileInput/../alignment/../general/userparams.h:8: In file included from fileInput/../alignment/../general/UserParameters.h:22: In file included from fileInput/../alignment/../general/utils.h:8: In file included from fileInput/../alignment/../general/Utility.h:15: In file included from fileInput/../alignment/../general/clustalw.h:44: fileInput/../alignment/../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -falign-functions=64 -Wall -g -O2 -c fileInput/GDEFileParser.cpp -o fileInput/GDEFileParser.o In file included from fileInput/GDEFileParser.cpp:16: In file included from fileInput/GDEFileParser.h:10: In file included from fileInput/FileParser.h:22: In file included from fileInput/../alignment/Sequence.h:20: In file included from fileInput/../alignment/../general/userparams.h:8: In file included from fileInput/../alignment/../general/UserParameters.h:22: In file included from fileInput/../alignment/../general/utils.h:8: In file included from fileInput/../alignment/../general/Utility.h:15: In file included from fileInput/../alignment/../general/clustalw.h:42: fileInput/../alignment/../general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from fileInput/GDEFileParser.cpp:16: In file included from fileInput/GDEFileParser.h:10: In file included from fileInput/FileParser.h:22: In file included from fileInput/../alignment/Sequence.h:20: In file included from fileInput/../alignment/../general/userparams.h:8: In file included from fileInput/../alignment/../general/UserParameters.h:22: In file included from fileInput/../alignment/../general/utils.h:8: In file included from fileInput/../alignment/../general/Utility.h:15: In file included from fileInput/../alignment/../general/clustalw.h:43: fileInput/../alignment/../general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from fileInput/GDEFileParser.cpp:16: In file included from fileInput/GDEFileParser.h:10: In file included from fileInput/FileParser.h:22: In file included from fileInput/../alignment/Sequence.h:20: In file included from fileInput/../alignment/../general/userparams.h:8: In file included from fileInput/../alignment/../general/UserParameters.h:22: In file included from fileInput/../alignment/../general/utils.h:8: In file included from fileInput/../alignment/../general/Utility.h:15: In file included from fileInput/../alignment/../general/clustalw.h:44: fileInput/../alignment/../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -falign-functions=64 -Wall -g -O2 -c fileInput/InFileStream.cpp -o fileInput/InFileStream.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -falign-functions=64 -Wall -g -O2 -c fileInput/ClustalFileParser.cpp -o fileInput/ClustalFileParser.o In file included from fileInput/ClustalFileParser.cpp:19: In file included from fileInput/ClustalFileParser.h:10: In file included from fileInput/FileParser.h:22: In file included from fileInput/../alignment/Sequence.h:20: In file included from fileInput/../alignment/../general/userparams.h:8: In file included from fileInput/../alignment/../general/UserParameters.h:22: In file included from fileInput/../alignment/../general/utils.h:8: In file included from fileInput/../alignment/../general/Utility.h:15: In file included from fileInput/../alignment/../general/clustalw.h:42: fileInput/../alignment/../general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from fileInput/ClustalFileParser.cpp:19: In file included from fileInput/ClustalFileParser.h:10: In file included from fileInput/FileParser.h:22: In file included from fileInput/../alignment/Sequence.h:20: In file included from fileInput/../alignment/../general/userparams.h:8: In file included from fileInput/../alignment/../general/UserParameters.h:22: In file included from fileInput/../alignment/../general/utils.h:8: In file included from fileInput/../alignment/../general/Utility.h:15: In file included from fileInput/../alignment/../general/clustalw.h:43: fileInput/../alignment/../general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from fileInput/ClustalFileParser.cpp:19: In file included from fileInput/ClustalFileParser.h:10: In file included from fileInput/FileParser.h:22: In file included from fileInput/../alignment/Sequence.h:20: In file included from fileInput/../alignment/../general/userparams.h:8: In file included from fileInput/../alignment/../general/UserParameters.h:22: In file included from fileInput/../alignment/../general/utils.h:8: In file included from fileInput/../alignment/../general/Utility.h:15: In file included from fileInput/../alignment/../general/clustalw.h:44: fileInput/../alignment/../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -falign-functions=64 -Wall -g -O2 -c fileInput/PearsonFileParser.cpp -o fileInput/PearsonFileParser.o In file included from fileInput/PearsonFileParser.cpp:26: In file included from fileInput/PearsonFileParser.h:14: In file included from fileInput/FileParser.h:22: In file included from fileInput/../alignment/Sequence.h:20: In file included from fileInput/../alignment/../general/userparams.h:8: In file included from fileInput/../alignment/../general/UserParameters.h:22: In file included from fileInput/../alignment/../general/utils.h:8: In file included from fileInput/../alignment/../general/Utility.h:15: In file included from fileInput/../alignment/../general/clustalw.h:42: fileInput/../alignment/../general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from fileInput/PearsonFileParser.cpp:26: In file included from fileInput/PearsonFileParser.h:14: In file included from fileInput/FileParser.h:22: In file included from fileInput/../alignment/Sequence.h:20: In file included from fileInput/../alignment/../general/userparams.h:8: In file included from fileInput/../alignment/../general/UserParameters.h:22: In file included from fileInput/../alignment/../general/utils.h:8: In file included from fileInput/../alignment/../general/Utility.h:15: In file included from fileInput/../alignment/../general/clustalw.h:43: fileInput/../alignment/../general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from fileInput/PearsonFileParser.cpp:26: In file included from fileInput/PearsonFileParser.h:14: In file included from fileInput/FileParser.h:22: In file included from fileInput/../alignment/Sequence.h:20: In file included from fileInput/../alignment/../general/userparams.h:8: In file included from fileInput/../alignment/../general/UserParameters.h:22: In file included from fileInput/../alignment/../general/utils.h:8: In file included from fileInput/../alignment/../general/Utility.h:15: In file included from fileInput/../alignment/../general/clustalw.h:44: fileInput/../alignment/../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -falign-functions=64 -Wall -g -O2 -c fileInput/FileParser.cpp -o fileInput/FileParser.o In file included from fileInput/FileParser.cpp:14: In file included from fileInput/FileParser.h:22: In file included from fileInput/../alignment/Sequence.h:20: In file included from fileInput/../alignment/../general/userparams.h:8: In file included from fileInput/../alignment/../general/UserParameters.h:22: In file included from fileInput/../alignment/../general/utils.h:8: In file included from fileInput/../alignment/../general/Utility.h:15: In file included from fileInput/../alignment/../general/clustalw.h:42: fileInput/../alignment/../general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from fileInput/FileParser.cpp:14: In file included from fileInput/FileParser.h:22: In file included from fileInput/../alignment/Sequence.h:20: In file included from fileInput/../alignment/../general/userparams.h:8: In file included from fileInput/../alignment/../general/UserParameters.h:22: In file included from fileInput/../alignment/../general/utils.h:8: In file included from fileInput/../alignment/../general/Utility.h:15: In file included from fileInput/../alignment/../general/clustalw.h:43: fileInput/../alignment/../general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ fileInput/FileParser.cpp:38:7: warning: unused variable 'n' [-Wunused-variable] int n = (*input).inputSeqs.size(); ^ In file included from fileInput/FileParser.cpp:14: In file included from fileInput/FileParser.h:22: In file included from fileInput/../alignment/Sequence.h:20: In file included from fileInput/../alignment/../general/userparams.h:8: In file included from fileInput/../alignment/../general/UserParameters.h:22: In file included from fileInput/../alignment/../general/utils.h:8: In file included from fileInput/../alignment/../general/Utility.h:15: In file included from fileInput/../alignment/../general/clustalw.h:44: fileInput/../alignment/../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 4 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -falign-functions=64 -Wall -g -O2 -c fileInput/EMBLFileParser.cpp -o fileInput/EMBLFileParser.o In file included from fileInput/EMBLFileParser.cpp:16: In file included from fileInput/EMBLFileParser.h:10: In file included from fileInput/FileParser.h:22: In file included from fileInput/../alignment/Sequence.h:20: In file included from fileInput/../alignment/../general/userparams.h:8: In file included from fileInput/../alignment/../general/UserParameters.h:22: In file included from fileInput/../alignment/../general/utils.h:8: In file included from fileInput/../alignment/../general/Utility.h:15: In file included from fileInput/../alignment/../general/clustalw.h:42: fileInput/../alignment/../general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from fileInput/EMBLFileParser.cpp:16: In file included from fileInput/EMBLFileParser.h:10: In file included from fileInput/FileParser.h:22: In file included from fileInput/../alignment/Sequence.h:20: In file included from fileInput/../alignment/../general/userparams.h:8: In file included from fileInput/../alignment/../general/UserParameters.h:22: In file included from fileInput/../alignment/../general/utils.h:8: In file included from fileInput/../alignment/../general/Utility.h:15: In file included from fileInput/../alignment/../general/clustalw.h:43: fileInput/../alignment/../general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from fileInput/EMBLFileParser.cpp:16: In file included from fileInput/EMBLFileParser.h:10: In file included from fileInput/FileParser.h:22: In file included from fileInput/../alignment/Sequence.h:20: In file included from fileInput/../alignment/../general/userparams.h:8: In file included from fileInput/../alignment/../general/UserParameters.h:22: In file included from fileInput/../alignment/../general/utils.h:8: In file included from fileInput/../alignment/../general/Utility.h:15: In file included from fileInput/../alignment/../general/clustalw.h:44: fileInput/../alignment/../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -falign-functions=64 -Wall -g -O2 -c tree/UPGMA/RootedClusterTree.cpp -o tree/UPGMA/RootedClusterTree.o In file included from tree/UPGMA/RootedClusterTree.cpp:9: In file included from tree/UPGMA/RootedClusterTree.h:8: In file included from tree/UPGMA/../ClusterTree.h:20: In file included from tree/UPGMA/../../alignment/Alignment.h:41: In file included from tree/UPGMA/../../alignment/Sequence.h:20: In file included from tree/UPGMA/../../alignment/../general/userparams.h:8: In file included from tree/UPGMA/../../alignment/../general/UserParameters.h:22: In file included from tree/UPGMA/../../alignment/../general/utils.h:8: In file included from tree/UPGMA/../../alignment/../general/Utility.h:15: In file included from tree/UPGMA/../../alignment/../general/clustalw.h:42: tree/UPGMA/../../alignment/../general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from tree/UPGMA/RootedClusterTree.cpp:9: In file included from tree/UPGMA/RootedClusterTree.h:8: In file included from tree/UPGMA/../ClusterTree.h:20: In file included from tree/UPGMA/../../alignment/Alignment.h:41: In file included from tree/UPGMA/../../alignment/Sequence.h:20: In file included from tree/UPGMA/../../alignment/../general/userparams.h:8: In file included from tree/UPGMA/../../alignment/../general/UserParameters.h:22: In file included from tree/UPGMA/../../alignment/../general/utils.h:8: In file included from tree/UPGMA/../../alignment/../general/Utility.h:15: In file included from tree/UPGMA/../../alignment/../general/clustalw.h:43: tree/UPGMA/../../alignment/../general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from tree/UPGMA/RootedClusterTree.cpp:9: In file included from tree/UPGMA/RootedClusterTree.h:8: In file included from tree/UPGMA/../ClusterTree.h:20: In file included from tree/UPGMA/../../alignment/Alignment.h:41: In file included from tree/UPGMA/../../alignment/Sequence.h:20: In file included from tree/UPGMA/../../alignment/../general/userparams.h:8: In file included from tree/UPGMA/../../alignment/../general/UserParameters.h:22: In file included from tree/UPGMA/../../alignment/../general/utils.h:8: In file included from tree/UPGMA/../../alignment/../general/Utility.h:15: In file included from tree/UPGMA/../../alignment/../general/clustalw.h:44: tree/UPGMA/../../alignment/../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -falign-functions=64 -Wall -g -O2 -c tree/UPGMA/UPGMAAlgorithm.cpp -o tree/UPGMA/UPGMAAlgorithm.o In file included from tree/UPGMA/UPGMAAlgorithm.cpp:4: In file included from tree/UPGMA/UPGMAAlgorithm.h:6: In file included from tree/UPGMA/../../general/clustalw.h:42: tree/UPGMA/../../general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from tree/UPGMA/UPGMAAlgorithm.cpp:4: In file included from tree/UPGMA/UPGMAAlgorithm.h:6: In file included from tree/UPGMA/../../general/clustalw.h:43: tree/UPGMA/../../general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from tree/UPGMA/UPGMAAlgorithm.cpp:4: In file included from tree/UPGMA/UPGMAAlgorithm.h:6: In file included from tree/UPGMA/../../general/clustalw.h:44: tree/UPGMA/../../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -falign-functions=64 -Wall -g -O2 -c tree/UPGMA/Node.cpp -o tree/UPGMA/Node.o In file included from tree/UPGMA/Node.cpp:7: In file included from tree/UPGMA/../../general/clustalw.h:42: tree/UPGMA/../../general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from tree/UPGMA/Node.cpp:7: In file included from tree/UPGMA/../../general/clustalw.h:43: tree/UPGMA/../../general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from tree/UPGMA/Node.cpp:7: In file included from tree/UPGMA/../../general/clustalw.h:44: tree/UPGMA/../../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -falign-functions=64 -Wall -g -O2 -c tree/UPGMA/RootedGuideTree.cpp -o tree/UPGMA/RootedGuideTree.o In file included from tree/UPGMA/RootedGuideTree.cpp:10: In file included from tree/UPGMA/RootedGuideTree.h:17: In file included from tree/UPGMA/../../alignment/Alignment.h:41: In file included from tree/UPGMA/../../alignment/Sequence.h:20: In file included from tree/UPGMA/../../alignment/../general/userparams.h:8: In file included from tree/UPGMA/../../alignment/../general/UserParameters.h:22: In file included from tree/UPGMA/../../alignment/../general/utils.h:8: In file included from tree/UPGMA/../../alignment/../general/Utility.h:15: In file included from tree/UPGMA/../../alignment/../general/clustalw.h:42: tree/UPGMA/../../alignment/../general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from tree/UPGMA/RootedGuideTree.cpp:10: In file included from tree/UPGMA/RootedGuideTree.h:17: In file included from tree/UPGMA/../../alignment/Alignment.h:41: In file included from tree/UPGMA/../../alignment/Sequence.h:20: In file included from tree/UPGMA/../../alignment/../general/userparams.h:8: In file included from tree/UPGMA/../../alignment/../general/UserParameters.h:22: In file included from tree/UPGMA/../../alignment/../general/utils.h:8: In file included from tree/UPGMA/../../alignment/../general/Utility.h:15: In file included from tree/UPGMA/../../alignment/../general/clustalw.h:43: tree/UPGMA/../../alignment/../general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from tree/UPGMA/RootedGuideTree.cpp:10: In file included from tree/UPGMA/RootedGuideTree.h:17: In file included from tree/UPGMA/../../alignment/Alignment.h:41: In file included from tree/UPGMA/../../alignment/Sequence.h:20: In file included from tree/UPGMA/../../alignment/../general/userparams.h:8: In file included from tree/UPGMA/../../alignment/../general/UserParameters.h:22: In file included from tree/UPGMA/../../alignment/../general/utils.h:8: In file included from tree/UPGMA/../../alignment/../general/Utility.h:15: In file included from tree/UPGMA/../../alignment/../general/clustalw.h:44: tree/UPGMA/../../alignment/../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -falign-functions=64 -Wall -g -O2 -c tree/UPGMA/RootedTreeOutput.cpp -o tree/UPGMA/RootedTreeOutput.o In file included from tree/UPGMA/RootedTreeOutput.cpp:9: In file included from tree/UPGMA/RootedTreeOutput.h:15: In file included from tree/UPGMA/RootedGuideTree.h:17: In file included from tree/UPGMA/../../alignment/Alignment.h:41: In file included from tree/UPGMA/../../alignment/Sequence.h:20: In file included from tree/UPGMA/../../alignment/../general/userparams.h:8: In file included from tree/UPGMA/../../alignment/../general/UserParameters.h:22: In file included from tree/UPGMA/../../alignment/../general/utils.h:8: In file included from tree/UPGMA/../../alignment/../general/Utility.h:15: In file included from tree/UPGMA/../../alignment/../general/clustalw.h:42: tree/UPGMA/../../alignment/../general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from tree/UPGMA/RootedTreeOutput.cpp:9: In file included from tree/UPGMA/RootedTreeOutput.h:15: In file included from tree/UPGMA/RootedGuideTree.h:17: In file included from tree/UPGMA/../../alignment/Alignment.h:41: In file included from tree/UPGMA/../../alignment/Sequence.h:20: In file included from tree/UPGMA/../../alignment/../general/userparams.h:8: In file included from tree/UPGMA/../../alignment/../general/UserParameters.h:22: In file included from tree/UPGMA/../../alignment/../general/utils.h:8: In file included from tree/UPGMA/../../alignment/../general/Utility.h:15: In file included from tree/UPGMA/../../alignment/../general/clustalw.h:43: tree/UPGMA/../../alignment/../general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from tree/UPGMA/RootedTreeOutput.cpp:9: In file included from tree/UPGMA/RootedTreeOutput.h:15: In file included from tree/UPGMA/RootedGuideTree.h:17: In file included from tree/UPGMA/../../alignment/Alignment.h:41: In file included from tree/UPGMA/../../alignment/Sequence.h:20: In file included from tree/UPGMA/../../alignment/../general/userparams.h:8: In file included from tree/UPGMA/../../alignment/../general/UserParameters.h:22: In file included from tree/UPGMA/../../alignment/../general/utils.h:8: In file included from tree/UPGMA/../../alignment/../general/Utility.h:15: In file included from tree/UPGMA/../../alignment/../general/clustalw.h:44: tree/UPGMA/../../alignment/../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -falign-functions=64 -Wall -g -O2 -c tree/Tree.cpp -o tree/Tree.o In file included from tree/Tree.cpp:10: In file included from tree/Tree.h:13: In file included from tree/../alignment/Alignment.h:41: In file included from tree/../alignment/Sequence.h:20: In file included from tree/../alignment/../general/userparams.h:8: In file included from tree/../alignment/../general/UserParameters.h:22: In file included from tree/../alignment/../general/utils.h:8: In file included from tree/../alignment/../general/Utility.h:15: In file included from tree/../alignment/../general/clustalw.h:42: tree/../alignment/../general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from tree/Tree.cpp:10: In file included from tree/Tree.h:13: In file included from tree/../alignment/Alignment.h:41: In file included from tree/../alignment/Sequence.h:20: In file included from tree/../alignment/../general/userparams.h:8: In file included from tree/../alignment/../general/UserParameters.h:22: In file included from tree/../alignment/../general/utils.h:8: In file included from tree/../alignment/../general/Utility.h:15: In file included from tree/../alignment/../general/clustalw.h:43: tree/../alignment/../general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from tree/Tree.cpp:10: In file included from tree/Tree.h:13: In file included from tree/../alignment/Alignment.h:41: In file included from tree/../alignment/Sequence.h:20: In file included from tree/../alignment/../general/userparams.h:8: In file included from tree/../alignment/../general/UserParameters.h:22: In file included from tree/../alignment/../general/utils.h:8: In file included from tree/../alignment/../general/Utility.h:15: In file included from tree/../alignment/../general/clustalw.h:44: tree/../alignment/../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -falign-functions=64 -Wall -g -O2 -c tree/ClusterTree.cpp -o tree/ClusterTree.o In file included from tree/ClusterTree.cpp:9: In file included from tree/ClusterTree.h:20: In file included from tree/../alignment/Alignment.h:41: In file included from tree/../alignment/Sequence.h:20: In file included from tree/../alignment/../general/userparams.h:8: In file included from tree/../alignment/../general/UserParameters.h:22: In file included from tree/../alignment/../general/utils.h:8: In file included from tree/../alignment/../general/Utility.h:15: In file included from tree/../alignment/../general/clustalw.h:42: tree/../alignment/../general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from tree/ClusterTree.cpp:9: In file included from tree/ClusterTree.h:20: In file included from tree/../alignment/Alignment.h:41: In file included from tree/../alignment/Sequence.h:20: In file included from tree/../alignment/../general/userparams.h:8: In file included from tree/../alignment/../general/UserParameters.h:22: In file included from tree/../alignment/../general/utils.h:8: In file included from tree/../alignment/../general/Utility.h:15: In file included from tree/../alignment/../general/clustalw.h:43: tree/../alignment/../general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ tree/ClusterTree.cpp:580:9: warning: variable 'rs' set but not used [-Wunused-but-set-variable] int rs = 0, rl = 0; ^ tree/ClusterTree.cpp:580:17: warning: variable 'rl' set but not used [-Wunused-but-set-variable] int rs = 0, rl = 0; ^ In file included from tree/ClusterTree.cpp:9: In file included from tree/ClusterTree.h:20: In file included from tree/../alignment/Alignment.h:41: In file included from tree/../alignment/Sequence.h:20: In file included from tree/../alignment/../general/userparams.h:8: In file included from tree/../alignment/../general/UserParameters.h:22: In file included from tree/../alignment/../general/utils.h:8: In file included from tree/../alignment/../general/Utility.h:15: In file included from tree/../alignment/../general/clustalw.h:44: tree/../alignment/../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 5 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -falign-functions=64 -Wall -g -O2 -c tree/TreeInterface.cpp -o tree/TreeInterface.o In file included from tree/TreeInterface.cpp:15: In file included from tree/TreeInterface.h:19: In file included from tree/../alignment/Alignment.h:41: In file included from tree/../alignment/Sequence.h:20: In file included from tree/../alignment/../general/userparams.h:8: In file included from tree/../alignment/../general/UserParameters.h:22: In file included from tree/../alignment/../general/utils.h:8: In file included from tree/../alignment/../general/Utility.h:15: In file included from tree/../alignment/../general/clustalw.h:42: tree/../alignment/../general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from tree/TreeInterface.cpp:15: In file included from tree/TreeInterface.h:19: In file included from tree/../alignment/Alignment.h:41: In file included from tree/../alignment/Sequence.h:20: In file included from tree/../alignment/../general/userparams.h:8: In file included from tree/../alignment/../general/UserParameters.h:22: In file included from tree/../alignment/../general/utils.h:8: In file included from tree/../alignment/../general/Utility.h:15: In file included from tree/../alignment/../general/clustalw.h:43: tree/../alignment/../general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from tree/TreeInterface.cpp:15: In file included from tree/TreeInterface.h:19: In file included from tree/../alignment/Alignment.h:41: In file included from tree/../alignment/Sequence.h:20: In file included from tree/../alignment/../general/userparams.h:8: In file included from tree/../alignment/../general/UserParameters.h:22: In file included from tree/../alignment/../general/utils.h:8: In file included from tree/../alignment/../general/Utility.h:15: In file included from tree/../alignment/../general/clustalw.h:44: tree/../alignment/../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -falign-functions=64 -Wall -g -O2 -c tree/UnRootedClusterTree.cpp -o tree/UnRootedClusterTree.o In file included from tree/UnRootedClusterTree.cpp:9: In file included from tree/UnRootedClusterTree.h:8: In file included from tree/ClusterTree.h:20: In file included from tree/../alignment/Alignment.h:41: In file included from tree/../alignment/Sequence.h:20: In file included from tree/../alignment/../general/userparams.h:8: In file included from tree/../alignment/../general/UserParameters.h:22: In file included from tree/../alignment/../general/utils.h:8: In file included from tree/../alignment/../general/Utility.h:15: In file included from tree/../alignment/../general/clustalw.h:42: tree/../alignment/../general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from tree/UnRootedClusterTree.cpp:9: In file included from tree/UnRootedClusterTree.h:8: In file included from tree/ClusterTree.h:20: In file included from tree/../alignment/Alignment.h:41: In file included from tree/../alignment/Sequence.h:20: In file included from tree/../alignment/../general/userparams.h:8: In file included from tree/../alignment/../general/UserParameters.h:22: In file included from tree/../alignment/../general/utils.h:8: In file included from tree/../alignment/../general/Utility.h:15: In file included from tree/../alignment/../general/clustalw.h:43: tree/../alignment/../general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from tree/UnRootedClusterTree.cpp:9: In file included from tree/UnRootedClusterTree.h:8: In file included from tree/ClusterTree.h:20: In file included from tree/../alignment/Alignment.h:41: In file included from tree/../alignment/Sequence.h:20: In file included from tree/../alignment/../general/userparams.h:8: In file included from tree/../alignment/../general/UserParameters.h:22: In file included from tree/../alignment/../general/utils.h:8: In file included from tree/../alignment/../general/Utility.h:15: In file included from tree/../alignment/../general/clustalw.h:44: tree/../alignment/../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -falign-functions=64 -Wall -g -O2 -c tree/ClusterTreeOutput.cpp -o tree/ClusterTreeOutput.o In file included from tree/ClusterTreeOutput.cpp:9: In file included from tree/ClusterTreeOutput.h:11: In file included from tree/../alignment/Alignment.h:41: In file included from tree/../alignment/Sequence.h:20: In file included from tree/../alignment/../general/userparams.h:8: In file included from tree/../alignment/../general/UserParameters.h:22: In file included from tree/../alignment/../general/utils.h:8: In file included from tree/../alignment/../general/Utility.h:15: In file included from tree/../alignment/../general/clustalw.h:42: tree/../alignment/../general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from tree/ClusterTreeOutput.cpp:9: In file included from tree/ClusterTreeOutput.h:11: In file included from tree/../alignment/Alignment.h:41: In file included from tree/../alignment/Sequence.h:20: In file included from tree/../alignment/../general/userparams.h:8: In file included from tree/../alignment/../general/UserParameters.h:22: In file included from tree/../alignment/../general/utils.h:8: In file included from tree/../alignment/../general/Utility.h:15: In file included from tree/../alignment/../general/clustalw.h:43: tree/../alignment/../general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from tree/ClusterTreeOutput.cpp:9: In file included from tree/ClusterTreeOutput.h:11: In file included from tree/../alignment/Alignment.h:41: In file included from tree/../alignment/Sequence.h:20: In file included from tree/../alignment/../general/userparams.h:8: In file included from tree/../alignment/../general/UserParameters.h:22: In file included from tree/../alignment/../general/utils.h:8: In file included from tree/../alignment/../general/Utility.h:15: In file included from tree/../alignment/../general/clustalw.h:44: tree/../alignment/../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -falign-functions=64 -Wall -g -O2 -c tree/RandomGenerator.cpp -o tree/RandomGenerator.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -falign-functions=64 -Wall -g -O2 -c tree/NJTree.cpp -o tree/NJTree.o In file included from tree/NJTree.cpp:10: In file included from tree/NJTree.h:11: In file included from tree/ClusterTreeAlgorithm.h:12: In file included from tree/../general/clustalw.h:42: tree/../general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from tree/NJTree.cpp:10: In file included from tree/NJTree.h:11: In file included from tree/ClusterTreeAlgorithm.h:12: In file included from tree/../general/clustalw.h:43: tree/../general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from tree/NJTree.cpp:10: In file included from tree/NJTree.h:11: In file included from tree/ClusterTreeAlgorithm.h:12: In file included from tree/../general/clustalw.h:44: tree/../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -falign-functions=64 -Wall -g -O2 -c tree/AlignmentSteps.cpp -o tree/AlignmentSteps.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -falign-functions=64 -Wall -g -O2 -c interface/CommandLineParser.cpp -o interface/CommandLineParser.o In file included from interface/CommandLineParser.cpp:13: In file included from interface/CommandLineParser.h:18: In file included from interface/../Clustal.h:15: In file included from ./general/clustalw.h:42: ./general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from interface/CommandLineParser.cpp:13: In file included from interface/CommandLineParser.h:18: In file included from interface/../Clustal.h:15: In file included from ./general/clustalw.h:43: ./general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from interface/CommandLineParser.cpp:13: In file included from interface/CommandLineParser.h:18: In file included from interface/../Clustal.h:15: In file included from ./general/clustalw.h:44: ./general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -falign-functions=64 -Wall -g -O2 -c substitutionMatrix/SubMatrix.cpp -o substitutionMatrix/SubMatrix.o In file included from substitutionMatrix/SubMatrix.cpp:15: In file included from substitutionMatrix/SubMatrix.h:28: In file included from substitutionMatrix/../general/clustalw.h:42: substitutionMatrix/../general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from substitutionMatrix/SubMatrix.cpp:15: In file included from substitutionMatrix/SubMatrix.h:28: In file included from substitutionMatrix/../general/clustalw.h:43: substitutionMatrix/../general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ substitutionMatrix/SubMatrix.cpp:175:17: warning: variable 'maxRes' set but not used [-Wunused-but-set-variable] short i, j, maxRes; ^ substitutionMatrix/SubMatrix.cpp:697:9: warning: variable 'av1' set but not used [-Wunused-but-set-variable] int av1, av2, av3, min, max; ^ substitutionMatrix/SubMatrix.cpp:1305:10: warning: unused variable 'inline1' [-Wunused-variable] char inline1[1024]; ^ substitutionMatrix/SubMatrix.cpp:1307:9: warning: unused variable 'nmat' [-Wunused-variable] int nmat; ^ substitutionMatrix/SubMatrix.cpp:1308:9: warning: unused variable 'n' [-Wunused-variable] int n, llimit, ulimit; ^ substitutionMatrix/SubMatrix.cpp:1308:12: warning: unused variable 'llimit' [-Wunused-variable] int n, llimit, ulimit; ^ substitutionMatrix/SubMatrix.cpp:1308:20: warning: unused variable 'ulimit' [-Wunused-variable] int n, llimit, ulimit; ^ substitutionMatrix/SubMatrix.cpp:1845:9: warning: variable 'maxRes' set but not used [-Wunused-but-set-variable] int maxRes; ^ substitutionMatrix/SubMatrix.cpp:1905:9: warning: variable 'maxRes' set but not used [-Wunused-but-set-variable] int maxRes; ^ In file included from substitutionMatrix/SubMatrix.cpp:15: In file included from substitutionMatrix/SubMatrix.h:28: In file included from substitutionMatrix/../general/clustalw.h:44: substitutionMatrix/../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 12 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -falign-functions=64 -Wall -g -O2 -c multipleAlign/Iteration.cpp -o multipleAlign/Iteration.o In file included from multipleAlign/Iteration.cpp:13: In file included from multipleAlign/Iteration.h:8: In file included from multipleAlign/../alignment/Alignment.h:41: In file included from multipleAlign/../alignment/Sequence.h:20: In file included from multipleAlign/../alignment/../general/userparams.h:8: In file included from multipleAlign/../alignment/../general/UserParameters.h:22: In file included from multipleAlign/../alignment/../general/utils.h:8: In file included from multipleAlign/../alignment/../general/Utility.h:15: In file included from multipleAlign/../alignment/../general/clustalw.h:42: multipleAlign/../alignment/../general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from multipleAlign/Iteration.cpp:13: In file included from multipleAlign/Iteration.h:8: In file included from multipleAlign/../alignment/Alignment.h:41: In file included from multipleAlign/../alignment/Sequence.h:20: In file included from multipleAlign/../alignment/../general/userparams.h:8: In file included from multipleAlign/../alignment/../general/UserParameters.h:22: In file included from multipleAlign/../alignment/../general/utils.h:8: In file included from multipleAlign/../alignment/../general/Utility.h:15: In file included from multipleAlign/../alignment/../general/clustalw.h:43: multipleAlign/../alignment/../general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ multipleAlign/Iteration.cpp:170:9: warning: variable 'count' set but not used [-Wunused-but-set-variable] int count; ^ In file included from multipleAlign/Iteration.cpp:13: In file included from multipleAlign/Iteration.h:8: In file included from multipleAlign/../alignment/Alignment.h:41: In file included from multipleAlign/../alignment/Sequence.h:20: In file included from multipleAlign/../alignment/../general/userparams.h:8: In file included from multipleAlign/../alignment/../general/UserParameters.h:22: In file included from multipleAlign/../alignment/../general/utils.h:8: In file included from multipleAlign/../alignment/../general/Utility.h:15: In file included from multipleAlign/../alignment/../general/clustalw.h:44: multipleAlign/../alignment/../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 4 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -falign-functions=64 -Wall -g -O2 -c multipleAlign/MSA.cpp -o multipleAlign/MSA.o In file included from multipleAlign/MSA.cpp:16: In file included from multipleAlign/MSA.h:10: In file included from multipleAlign/ProfileBase.h:14: In file included from multipleAlign/../alignment/Alignment.h:41: In file included from multipleAlign/../alignment/Sequence.h:20: In file included from multipleAlign/../alignment/../general/userparams.h:8: In file included from multipleAlign/../alignment/../general/UserParameters.h:22: In file included from multipleAlign/../alignment/../general/utils.h:8: In file included from multipleAlign/../alignment/../general/Utility.h:15: In file included from multipleAlign/../alignment/../general/clustalw.h:42: multipleAlign/../alignment/../general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from multipleAlign/MSA.cpp:16: In file included from multipleAlign/MSA.h:10: In file included from multipleAlign/ProfileBase.h:14: In file included from multipleAlign/../alignment/Alignment.h:41: In file included from multipleAlign/../alignment/Sequence.h:20: In file included from multipleAlign/../alignment/../general/userparams.h:8: In file included from multipleAlign/../alignment/../general/UserParameters.h:22: In file included from multipleAlign/../alignment/../general/utils.h:8: In file included from multipleAlign/../alignment/../general/Utility.h:15: In file included from multipleAlign/../alignment/../general/clustalw.h:43: multipleAlign/../alignment/../general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ multipleAlign/MSA.cpp:340:11: warning: unused variable 'alignmentScore' [-Wunused-variable] int alignmentScore = alnPtr->alignScore(); // ?? check, FS, 2009-05-18 ^ multipleAlign/MSA.cpp:369:18: warning: variable 'entries' set but not used [-Wunused-but-set-variable] int sum = 0, entries = 0; ^ In file included from multipleAlign/MSA.cpp:16: In file included from multipleAlign/MSA.h:10: In file included from multipleAlign/ProfileBase.h:14: In file included from multipleAlign/../alignment/Alignment.h:41: In file included from multipleAlign/../alignment/Sequence.h:20: In file included from multipleAlign/../alignment/../general/userparams.h:8: In file included from multipleAlign/../alignment/../general/UserParameters.h:22: In file included from multipleAlign/../alignment/../general/utils.h:8: In file included from multipleAlign/../alignment/../general/Utility.h:15: In file included from multipleAlign/../alignment/../general/clustalw.h:44: multipleAlign/../alignment/../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 5 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -falign-functions=64 -Wall -g -O2 -c multipleAlign/MyersMillerProfileAlign.cpp -o multipleAlign/MyersMillerProfileAlign.o In file included from multipleAlign/MyersMillerProfileAlign.cpp:10: In file included from multipleAlign/MyersMillerProfileAlign.h:10: In file included from multipleAlign/ProfileAlignAlgorithm.h:10: In file included from multipleAlign/../alignment/Alignment.h:41: In file included from multipleAlign/../alignment/Sequence.h:20: In file included from multipleAlign/../alignment/../general/userparams.h:8: In file included from multipleAlign/../alignment/../general/UserParameters.h:22: In file included from multipleAlign/../alignment/../general/utils.h:8: In file included from multipleAlign/../alignment/../general/Utility.h:15: In file included from multipleAlign/../alignment/../general/clustalw.h:42: multipleAlign/../alignment/../general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from multipleAlign/MyersMillerProfileAlign.cpp:10: In file included from multipleAlign/MyersMillerProfileAlign.h:10: In file included from multipleAlign/ProfileAlignAlgorithm.h:10: In file included from multipleAlign/../alignment/Alignment.h:41: In file included from multipleAlign/../alignment/Sequence.h:20: In file included from multipleAlign/../alignment/../general/userparams.h:8: In file included from multipleAlign/../alignment/../general/UserParameters.h:22: In file included from multipleAlign/../alignment/../general/utils.h:8: In file included from multipleAlign/../alignment/../general/Utility.h:15: In file included from multipleAlign/../alignment/../general/clustalw.h:43: multipleAlign/../alignment/../general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from multipleAlign/MyersMillerProfileAlign.cpp:10: In file included from multipleAlign/MyersMillerProfileAlign.h:10: In file included from multipleAlign/ProfileAlignAlgorithm.h:10: In file included from multipleAlign/../alignment/Alignment.h:41: In file included from multipleAlign/../alignment/Sequence.h:20: In file included from multipleAlign/../alignment/../general/userparams.h:8: In file included from multipleAlign/../alignment/../general/UserParameters.h:22: In file included from multipleAlign/../alignment/../general/utils.h:8: In file included from multipleAlign/../alignment/../general/Utility.h:15: In file included from multipleAlign/../alignment/../general/clustalw.h:44: multipleAlign/../alignment/../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ In file included from multipleAlign/MyersMillerProfileAlign.cpp:10: multipleAlign/MyersMillerProfileAlign.h:60:13: warning: private field 'matrix' is not used [-Wunused-private-field] int matrix[32][32]; ^ 4 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -falign-functions=64 -Wall -g -O2 -c multipleAlign/ProfileStandard.cpp -o multipleAlign/ProfileStandard.o In file included from multipleAlign/ProfileStandard.cpp:9: In file included from multipleAlign/ProfileStandard.h:9: In file included from multipleAlign/../alignment/Alignment.h:41: In file included from multipleAlign/../alignment/Sequence.h:20: In file included from multipleAlign/../alignment/../general/userparams.h:8: In file included from multipleAlign/../alignment/../general/UserParameters.h:22: In file included from multipleAlign/../alignment/../general/utils.h:8: In file included from multipleAlign/../alignment/../general/Utility.h:15: In file included from multipleAlign/../alignment/../general/clustalw.h:42: multipleAlign/../alignment/../general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from multipleAlign/ProfileStandard.cpp:9: In file included from multipleAlign/ProfileStandard.h:9: In file included from multipleAlign/../alignment/Alignment.h:41: In file included from multipleAlign/../alignment/Sequence.h:20: In file included from multipleAlign/../alignment/../general/userparams.h:8: In file included from multipleAlign/../alignment/../general/UserParameters.h:22: In file included from multipleAlign/../alignment/../general/utils.h:8: In file included from multipleAlign/../alignment/../general/Utility.h:15: In file included from multipleAlign/../alignment/../general/clustalw.h:43: multipleAlign/../alignment/../general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from multipleAlign/ProfileStandard.cpp:9: In file included from multipleAlign/ProfileStandard.h:9: In file included from multipleAlign/../alignment/Alignment.h:41: In file included from multipleAlign/../alignment/Sequence.h:20: In file included from multipleAlign/../alignment/../general/userparams.h:8: In file included from multipleAlign/../alignment/../general/UserParameters.h:22: In file included from multipleAlign/../alignment/../general/utils.h:8: In file included from multipleAlign/../alignment/../general/Utility.h:15: In file included from multipleAlign/../alignment/../general/clustalw.h:44: multipleAlign/../alignment/../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -falign-functions=64 -Wall -g -O2 -c multipleAlign/ProfileWithSub.cpp -o multipleAlign/ProfileWithSub.o In file included from multipleAlign/ProfileWithSub.cpp:9: In file included from multipleAlign/ProfileWithSub.h:9: In file included from multipleAlign/../alignment/Alignment.h:41: In file included from multipleAlign/../alignment/Sequence.h:20: In file included from multipleAlign/../alignment/../general/userparams.h:8: In file included from multipleAlign/../alignment/../general/UserParameters.h:22: In file included from multipleAlign/../alignment/../general/utils.h:8: In file included from multipleAlign/../alignment/../general/Utility.h:15: In file included from multipleAlign/../alignment/../general/clustalw.h:42: multipleAlign/../alignment/../general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from multipleAlign/ProfileWithSub.cpp:9: In file included from multipleAlign/ProfileWithSub.h:9: In file included from multipleAlign/../alignment/Alignment.h:41: In file included from multipleAlign/../alignment/Sequence.h:20: In file included from multipleAlign/../alignment/../general/userparams.h:8: In file included from multipleAlign/../alignment/../general/UserParameters.h:22: In file included from multipleAlign/../alignment/../general/utils.h:8: In file included from multipleAlign/../alignment/../general/Utility.h:15: In file included from multipleAlign/../alignment/../general/clustalw.h:43: multipleAlign/../alignment/../general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from multipleAlign/ProfileWithSub.cpp:9: In file included from multipleAlign/ProfileWithSub.h:9: In file included from multipleAlign/../alignment/Alignment.h:41: In file included from multipleAlign/../alignment/Sequence.h:20: In file included from multipleAlign/../alignment/../general/userparams.h:8: In file included from multipleAlign/../alignment/../general/UserParameters.h:22: In file included from multipleAlign/../alignment/../general/utils.h:8: In file included from multipleAlign/../alignment/../general/Utility.h:15: In file included from multipleAlign/../alignment/../general/clustalw.h:44: multipleAlign/../alignment/../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -falign-functions=64 -Wall -g -O2 -c multipleAlign/ProfileBase.cpp -o multipleAlign/ProfileBase.o In file included from multipleAlign/ProfileBase.cpp:9: In file included from multipleAlign/ProfileBase.h:14: In file included from multipleAlign/../alignment/Alignment.h:41: In file included from multipleAlign/../alignment/Sequence.h:20: In file included from multipleAlign/../alignment/../general/userparams.h:8: In file included from multipleAlign/../alignment/../general/UserParameters.h:22: In file included from multipleAlign/../alignment/../general/utils.h:8: In file included from multipleAlign/../alignment/../general/Utility.h:15: In file included from multipleAlign/../alignment/../general/clustalw.h:42: multipleAlign/../alignment/../general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from multipleAlign/ProfileBase.cpp:9: In file included from multipleAlign/ProfileBase.h:14: In file included from multipleAlign/../alignment/Alignment.h:41: In file included from multipleAlign/../alignment/Sequence.h:20: In file included from multipleAlign/../alignment/../general/userparams.h:8: In file included from multipleAlign/../alignment/../general/UserParameters.h:22: In file included from multipleAlign/../alignment/../general/utils.h:8: In file included from multipleAlign/../alignment/../general/Utility.h:15: In file included from multipleAlign/../alignment/../general/clustalw.h:43: multipleAlign/../alignment/../general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from multipleAlign/ProfileBase.cpp:9: In file included from multipleAlign/ProfileBase.h:14: In file included from multipleAlign/../alignment/Alignment.h:41: In file included from multipleAlign/../alignment/Sequence.h:20: In file included from multipleAlign/../alignment/../general/userparams.h:8: In file included from multipleAlign/../alignment/../general/UserParameters.h:22: In file included from multipleAlign/../alignment/../general/utils.h:8: In file included from multipleAlign/../alignment/../general/Utility.h:15: In file included from multipleAlign/../alignment/../general/clustalw.h:44: multipleAlign/../alignment/../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -falign-functions=64 -Wall -g -O2 -c multipleAlign/LowScoreSegProfile.cpp -o multipleAlign/LowScoreSegProfile.o In file included from multipleAlign/LowScoreSegProfile.cpp:9: In file included from multipleAlign/LowScoreSegProfile.h:13: In file included from multipleAlign/../alignment/Alignment.h:41: In file included from multipleAlign/../alignment/Sequence.h:20: In file included from multipleAlign/../alignment/../general/userparams.h:8: In file included from multipleAlign/../alignment/../general/UserParameters.h:22: In file included from multipleAlign/../alignment/../general/utils.h:8: In file included from multipleAlign/../alignment/../general/Utility.h:15: In file included from multipleAlign/../alignment/../general/clustalw.h:42: multipleAlign/../alignment/../general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from multipleAlign/LowScoreSegProfile.cpp:9: In file included from multipleAlign/LowScoreSegProfile.h:13: In file included from multipleAlign/../alignment/Alignment.h:41: In file included from multipleAlign/../alignment/Sequence.h:20: In file included from multipleAlign/../alignment/../general/userparams.h:8: In file included from multipleAlign/../alignment/../general/UserParameters.h:22: In file included from multipleAlign/../alignment/../general/utils.h:8: In file included from multipleAlign/../alignment/../general/Utility.h:15: In file included from multipleAlign/../alignment/../general/clustalw.h:43: multipleAlign/../alignment/../general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from multipleAlign/LowScoreSegProfile.cpp:9: In file included from multipleAlign/LowScoreSegProfile.h:13: In file included from multipleAlign/../alignment/Alignment.h:41: In file included from multipleAlign/../alignment/Sequence.h:20: In file included from multipleAlign/../alignment/../general/userparams.h:8: In file included from multipleAlign/../alignment/../general/UserParameters.h:22: In file included from multipleAlign/../alignment/../general/utils.h:8: In file included from multipleAlign/../alignment/../general/Utility.h:15: In file included from multipleAlign/../alignment/../general/clustalw.h:44: multipleAlign/../alignment/../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -falign-functions=64 -Wall -g -O2 -c general/OutputFile.cpp -o general/OutputFile.o In file included from general/OutputFile.cpp:10: In file included from general/utils.h:8: In file included from general/Utility.h:15: In file included from general/clustalw.h:42: general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from general/OutputFile.cpp:10: In file included from general/utils.h:8: In file included from general/Utility.h:15: In file included from general/clustalw.h:43: general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from general/OutputFile.cpp:10: In file included from general/utils.h:8: In file included from general/Utility.h:15: In file included from general/clustalw.h:44: general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -falign-functions=64 -Wall -g -O2 -c general/UserParameters.cpp -o general/UserParameters.o In file included from general/UserParameters.cpp:24: In file included from general/UserParameters.h:22: In file included from general/utils.h:8: In file included from general/Utility.h:15: In file included from general/clustalw.h:42: general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from general/UserParameters.cpp:24: In file included from general/UserParameters.h:22: In file included from general/utils.h:8: In file included from general/Utility.h:15: In file included from general/clustalw.h:43: general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from general/UserParameters.cpp:24: In file included from general/UserParameters.h:22: In file included from general/utils.h:8: In file included from general/Utility.h:15: In file included from general/clustalw.h:44: general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -falign-functions=64 -Wall -g -O2 -c general/Utility.cpp -o general/Utility.o In file included from general/Utility.cpp:19: In file included from general/Utility.h:15: In file included from general/clustalw.h:42: general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from general/Utility.cpp:19: In file included from general/Utility.h:15: In file included from general/clustalw.h:43: general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ general/Utility.cpp:251:8: warning: variable 'n' set but not used [-Wunused-but-set-variable] int n; ^ In file included from general/Utility.cpp:19: In file included from general/Utility.h:15: In file included from general/clustalw.h:44: general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 4 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -falign-functions=64 -Wall -g -O2 -c general/InvalidCombination.cpp -o general/InvalidCombination.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -falign-functions=64 -Wall -g -O2 -c general/DebugLog.cpp -o general/DebugLog.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -falign-functions=64 -Wall -g -O2 -c general/ClustalWResources.cpp -o general/ClustalWResources.o In file included from general/ClustalWResources.cpp:14: In file included from general/clustalw.h:42: general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from general/ClustalWResources.cpp:14: In file included from general/clustalw.h:43: general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from general/ClustalWResources.cpp:14: In file included from general/clustalw.h:44: general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -falign-functions=64 -Wall -g -O2 -c general/VectorOutOfRange.cpp -o general/VectorOutOfRange.o general/VectorOutOfRange.cpp:28:12: warning: address of stack memory associated with local variable 'outputMessage' returned [-Wreturn-stack-address] return outputMessage.c_str(); ^~~~~~~~~~~~~ general/VectorOutOfRange.cpp:37:12: warning: address of stack memory associated with local variable 'outputMessage' returned [-Wreturn-stack-address] return outputMessage.c_str(); ^~~~~~~~~~~~~ 2 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -falign-functions=64 -Wall -g -O2 -c general/SymMatrix.cpp -o general/SymMatrix.o In file included from general/SymMatrix.cpp:10: general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -falign-functions=64 -Wall -g -O2 -c general/Stats.cpp -o general/Stats.o In file included from general/Stats.cpp:15: In file included from general/../alignment/Alignment.h:41: In file included from general/../alignment/Sequence.h:20: In file included from general/../alignment/../general/userparams.h:8: In file included from general/UserParameters.h:22: In file included from general/utils.h:8: In file included from general/Utility.h:15: In file included from general/clustalw.h:42: general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from general/Stats.cpp:15: In file included from general/../alignment/Alignment.h:41: In file included from general/../alignment/Sequence.h:20: In file included from general/../alignment/../general/userparams.h:8: In file included from general/UserParameters.h:22: In file included from general/utils.h:8: In file included from general/Utility.h:15: In file included from general/clustalw.h:43: general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from general/Stats.cpp:15: In file included from general/../alignment/Alignment.h:41: In file included from general/../alignment/Sequence.h:20: In file included from general/../alignment/../general/userparams.h:8: In file included from general/UserParameters.h:22: In file included from general/utils.h:8: In file included from general/Utility.h:15: In file included from general/clustalw.h:44: general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -falign-functions=64 -Wall -g -O2 -c Help.cpp -o Help.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -falign-functions=64 -Wall -g -O2 -c alignment/Alignment.cpp -o alignment/Alignment.o In file included from alignment/Alignment.cpp:25: In file included from alignment/Alignment.h:41: In file included from alignment/Sequence.h:20: In file included from alignment/../general/userparams.h:8: In file included from alignment/../general/UserParameters.h:22: In file included from alignment/../general/utils.h:8: In file included from alignment/../general/Utility.h:15: In file included from alignment/../general/clustalw.h:42: alignment/../general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from alignment/Alignment.cpp:25: In file included from alignment/Alignment.h:41: In file included from alignment/Sequence.h:20: In file included from alignment/../general/userparams.h:8: In file included from alignment/../general/UserParameters.h:22: In file included from alignment/../general/utils.h:8: In file included from alignment/../general/Utility.h:15: In file included from alignment/../general/clustalw.h:43: alignment/../general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ alignment/Alignment.cpp:819:9: warning: variable 'counter2' set but not used [-Wunused-but-set-variable] int counter2 = 2; ^ alignment/Alignment.cpp:1715:24: warning: unused variable 'posToAddTo' [-Wunused-variable] SeqArray::iterator posToAddTo = sectionToRealign.begin(); ^ In file included from alignment/Alignment.cpp:25: In file included from alignment/Alignment.h:41: In file included from alignment/Sequence.h:20: In file included from alignment/../general/userparams.h:8: In file included from alignment/../general/UserParameters.h:22: In file included from alignment/../general/utils.h:8: In file included from alignment/../general/Utility.h:15: In file included from alignment/../general/clustalw.h:44: alignment/../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 5 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -falign-functions=64 -Wall -g -O2 -c alignment/AlignmentOutput.cpp -o alignment/AlignmentOutput.o In file included from alignment/AlignmentOutput.cpp:27: In file included from alignment/AlignmentOutput.h:24: In file included from alignment/Alignment.h:41: In file included from alignment/Sequence.h:20: In file included from alignment/../general/userparams.h:8: In file included from alignment/../general/UserParameters.h:22: In file included from alignment/../general/utils.h:8: In file included from alignment/../general/Utility.h:15: In file included from alignment/../general/clustalw.h:42: alignment/../general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from alignment/AlignmentOutput.cpp:27: In file included from alignment/AlignmentOutput.h:24: In file included from alignment/Alignment.h:41: In file included from alignment/Sequence.h:20: In file included from alignment/../general/userparams.h:8: In file included from alignment/../general/UserParameters.h:22: In file included from alignment/../general/utils.h:8: In file included from alignment/../general/Utility.h:15: In file included from alignment/../general/clustalw.h:43: alignment/../general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ alignment/AlignmentOutput.cpp:2297:16: warning: variable 'slen' set but not used [-Wunused-but-set-variable] int j, slen; ^ In file included from alignment/AlignmentOutput.cpp:27: In file included from alignment/AlignmentOutput.h:24: In file included from alignment/Alignment.h:41: In file included from alignment/Sequence.h:20: In file included from alignment/../general/userparams.h:8: In file included from alignment/../general/UserParameters.h:22: In file included from alignment/../general/utils.h:8: In file included from alignment/../general/Utility.h:15: In file included from alignment/../general/clustalw.h:44: alignment/../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 4 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -falign-functions=64 -Wall -g -O2 -c alignment/ObjectiveScore.cpp -o alignment/ObjectiveScore.o In file included from alignment/ObjectiveScore.cpp:10: In file included from alignment/ObjectiveScore.h:14: In file included from alignment/../general/clustalw.h:42: alignment/../general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from alignment/ObjectiveScore.cpp:10: In file included from alignment/ObjectiveScore.h:14: In file included from alignment/../general/clustalw.h:43: alignment/../general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from alignment/ObjectiveScore.cpp:10: In file included from alignment/ObjectiveScore.h:14: In file included from alignment/../general/clustalw.h:44: alignment/../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ In file included from alignment/ObjectiveScore.cpp:10: alignment/ObjectiveScore.h:40:14: warning: private field 'scale' is not used [-Wunused-private-field] long scale; ^ alignment/ObjectiveScore.h:41:13: warning: private field 'weightScale' is not used [-Wunused-private-field] int weightScale; ^ alignment/ObjectiveScore.h:42:13: warning: private field 'sagaGapEx' is not used [-Wunused-private-field] int sagaGapEx, sagaGapOp; ^ alignment/ObjectiveScore.h:42:24: warning: private field 'sagaGapOp' is not used [-Wunused-private-field] int sagaGapEx, sagaGapOp; ^ 7 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -falign-functions=64 -Wall -g -O2 -c alignment/Sequence.cpp -o alignment/Sequence.o In file included from alignment/Sequence.cpp:10: In file included from alignment/Sequence.h:20: In file included from alignment/../general/userparams.h:8: In file included from alignment/../general/UserParameters.h:22: In file included from alignment/../general/utils.h:8: In file included from alignment/../general/Utility.h:15: In file included from alignment/../general/clustalw.h:42: alignment/../general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from alignment/Sequence.cpp:10: In file included from alignment/Sequence.h:20: In file included from alignment/../general/userparams.h:8: In file included from alignment/../general/UserParameters.h:22: In file included from alignment/../general/utils.h:8: In file included from alignment/../general/Utility.h:15: In file included from alignment/../general/clustalw.h:43: alignment/../general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from alignment/Sequence.cpp:10: In file included from alignment/Sequence.h:20: In file included from alignment/../general/userparams.h:8: In file included from alignment/../general/UserParameters.h:22: In file included from alignment/../general/utils.h:8: In file included from alignment/../general/Utility.h:15: In file included from alignment/../general/clustalw.h:44: alignment/../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -falign-functions=64 -Wall -g -O2 -c Clustal.cpp -o Clustal.o In file included from Clustal.cpp:27: In file included from ./Clustal.h:15: In file included from ./general/clustalw.h:42: ./general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from Clustal.cpp:27: In file included from ./Clustal.h:15: In file included from ./general/clustalw.h:43: ./general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from Clustal.cpp:27: In file included from ./Clustal.h:15: In file included from ./general/clustalw.h:44: ./general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -falign-functions=64 -Wall -g -O2 -c RClustalWMain.cpp -o RClustalWMain.o In file included from RClustalWMain.cpp:5: In file included from ./alignment/Alignment.h:41: In file included from ./alignment/Sequence.h:20: In file included from ./alignment/../general/userparams.h:8: In file included from ./alignment/../general/UserParameters.h:22: In file included from ./alignment/../general/utils.h:8: In file included from ./alignment/../general/Utility.h:15: In file included from ./alignment/../general/clustalw.h:42: ./alignment/../general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from RClustalWMain.cpp:5: In file included from ./alignment/Alignment.h:41: In file included from ./alignment/Sequence.h:20: In file included from ./alignment/../general/userparams.h:8: In file included from ./alignment/../general/UserParameters.h:22: In file included from ./alignment/../general/utils.h:8: In file included from ./alignment/../general/Utility.h:15: In file included from ./alignment/../general/clustalw.h:43: ./alignment/../general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from RClustalWMain.cpp:5: In file included from ./alignment/Alignment.h:41: In file included from ./alignment/Sequence.h:20: In file included from ./alignment/../general/userparams.h:8: In file included from ./alignment/../general/UserParameters.h:22: In file included from ./alignment/../general/utils.h:8: In file included from ./alignment/../general/Utility.h:15: In file included from ./alignment/../general/clustalw.h:44: ./alignment/../general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -DHAVE_CONFIG_H -std=c++14 -I. -Wno-deprecated -Wno-unused-result -fPIC -falign-functions=64 -Wall -g -O2 -c RClustalW.cpp -o RClustalW.o In file included from RClustalW.cpp:2: In file included from ./RClustalWMain.h:6: In file included from ./general/clustalw.h:42: ./general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from RClustalW.cpp:2: In file included from ./RClustalWMain.h:6: In file included from ./general/clustalw.h:43: ./general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable] int y = x.size(); ^ In file included from RClustalW.cpp:2: In file included from ./RClustalWMain.h:6: In file included from ./general/clustalw.h:44: ./general/SymMatrix.h:291:13: warning: private field 'firstSeq' is not used [-Wunused-private-field] int firstSeq, numSeqsInSub; ^ 3 warnings generated. 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 libClustalW.so pairwise/FullPairwiseAlign.o pairwise/FastPairwiseAlign.o fileInput/MSFFileParser.o fileInput/FileReader.o fileInput/PIRFileParser.o fileInput/RSFFileParser.o fileInput/GDEFileParser.o fileInput/InFileStream.o fileInput/ClustalFileParser.o fileInput/PearsonFileParser.o fileInput/FileParser.o fileInput/EMBLFileParser.o tree/UPGMA/RootedClusterTree.o tree/UPGMA/UPGMAAlgorithm.o tree/UPGMA/Node.o tree/UPGMA/RootedGuideTree.o tree/UPGMA/RootedTreeOutput.o tree/Tree.o tree/ClusterTree.o tree/TreeInterface.o tree/UnRootedClusterTree.o tree/ClusterTreeOutput.o tree/RandomGenerator.o tree/NJTree.o tree/AlignmentSteps.o interface/CommandLineParser.o substitutionMatrix/SubMatrix.o multipleAlign/Iteration.o multipleAlign/MSA.o multipleAlign/MyersMillerProfileAlign.o multipleAlign/ProfileStandard.o multipleAlign/ProfileWithSub.o multipleAlign/ProfileBase.o multipleAlign/LowScoreSegProfile.o general/OutputFile.o general/UserParameters.o general/Utility.o general/InvalidCombination.o general/DebugLog.o general/ClustalWResources.o general/VectorOutOfRange.o general/SymMatrix.o general/Stats.o Help.o alignment/Alignment.o alignment/AlignmentOutput.o alignment/ObjectiveScore.o alignment/Sequence.o Clustal.o RClustalWMain.o RClustalW.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation ---------------------------------------- --------------- ClustalW --------------- ---------------------------------------- --------- Compilation finished --------- ---------------------------------------- make --file=msaMakefile --directory=ClustalOmega ./configure `/Library/Frameworks/R.framework/Resources/bin/Rscript -e "if (Sys.info()['sysname'] == 'Darwin') cat('--without-openmp')"`; \ export PKG_LIBS=" "; \ export PKG_CXXFLAGS=" `/Library/Frameworks/R.framework/Resources/bin/Rscript -e "if (Sys.info()['sysname'] == 'Darwin') cat('-DMATH_H_CLIB')"` -std=c++11 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include"; \ export PKG_CFLAGS=" -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include"; \ cd src; \ /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB -o libClustalOmega.so exceptions4c/e4c_lite.c argtable2/argtable2.c argtable2/arg_end.c argtable2/arg_rem.c argtable2/arg_lit.c argtable2/arg_int.c argtable2/arg_dbl.c argtable2/arg_str.c argtable2/arg_file.c kmpp/KMeans.cpp kmpp/KmTree.cpp kmpp/KmUtils.cpp clustal/hhalign_wrapper.c clustal/ktuple_pair.c clustal/list.c clustal/log.c clustal/muscle_upgma.c clustal/muscle_tree.c clustal/mbed.c clustal/pair_dist.c clustal/progress.c clustal/seq.c clustal/symmatrix.c clustal/tree.c clustal/util.c clustal/weights.c squid/a2m.c squid/aligneval.c squid/alignio.c squid/clustal.c squid/cluster.c squid/dayhoff.c squid/eps.c squid/file.c squid/getopt.c squid/gki.c squid/gsi.c squid/gsi64.c squid/hsregex.c squid/iupac.c squid/msa.c squid/msf.c squid/phylip.c squid/revcomp.c squid/rk.c squid/selex.c squid/seqencode.c squid/shuffle.c squid/sqerror.c squid/sqio.c squid/squidcore.c squid/sre_ctype.c squid/sre_math.c squid/sre_random.c squid/sre_string.c squid/ssi.c squid/stack.c squid/stockholm.c squid/stopwatch.c squid/translate.c squid/types.c squid/vectorops.c squid/weight.c hhalign/hhalign.cpp RClustalOmega.cpp mymain.c clustal-omega.c && \ ar rcs libClustalOmega.a exceptions4c/e4c_lite.o argtable2/argtable2.o argtable2/arg_end.o argtable2/arg_rem.o argtable2/arg_lit.o argtable2/arg_int.o argtable2/arg_dbl.o argtable2/arg_str.o argtable2/arg_file.o kmpp/KMeans.o kmpp/KmTree.o kmpp/KmUtils.o clustal/hhalign_wrapper.o clustal/ktuple_pair.o clustal/list.o clustal/log.o clustal/muscle_upgma.o clustal/muscle_tree.o clustal/mbed.o clustal/pair_dist.o clustal/progress.o clustal/seq.o clustal/symmatrix.o clustal/tree.o clustal/util.o clustal/weights.o squid/a2m.o squid/aligneval.o squid/alignio.o squid/clustal.o squid/cluster.o squid/dayhoff.o squid/eps.o squid/file.o squid/getopt.o squid/gki.o squid/gsi.o squid/gsi64.o squid/hsregex.o squid/iupac.o squid/msa.o squid/msf.o squid/phylip.o squid/revcomp.o squid/rk.o squid/selex.o squid/seqencode.o squid/shuffle.o squid/sqerror.o squid/sqio.o squid/squidcore.o squid/sre_ctype.o squid/sre_math.o squid/sre_random.o squid/sre_string.o squid/ssi.o squid/stack.o squid/stockholm.o squid/stopwatch.o squid/translate.o squid/types.o squid/vectorops.o squid/weight.o hhalign/hhalign.o RClustalOmega.o mymain.o clustal-omega.o && \ cp libClustalOmega.a ../../ configure: Welcome to Clustal Omega - version 1.2.0 (AndreaGiacomo) +NMMMMMMMMMS= MMMMM? :MMMMM8 IMMMMS MMMMM, ~MMMMN ,MMMMM =MMMMM MMMMM ?MMMMM +MMMMM MMMMMS MMMMM MMMMM MMMMM: MMMMM MMMMM+ MMMMM MMMMM~ MMMMM MMMMM MMMMMZ MMMMM MMMMM ,MMMMZ MMMM8 MMMM+ MMMMS MMMM, MMMMO MMMM ,N SMMM MMM8 +8 ,M7 M+ M+ :M8 ,MMMMMMMMMMMMI MMMMMMMMMMMM8 ,MMMMMMMMMMMM8 MMMMMMMMMMMM8 ,MMMMMMMMMMMMN MMMMMMMMMMMM8 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 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 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 minix/config.h usability... no checking minix/config.h presence... no checking for minix/config.h... no checking whether it is safe to define __EXTENSIONS__... yes checking build system type... aarch64-apple-darwin22.6.0 checking host system type... aarch64-apple-darwin22.6.0 checking whether make sets $(MAKE)... (cached) yes checking for a sed that does not truncate output... /usr/bin/sed checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... /Library/Developer/CommandLineTools/usr/bin/ld checking if the linker (/Library/Developer/CommandLineTools/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 whether the shell understands some XSI constructs... yes checking whether the shell understands "+="... yes checking for /Library/Developer/CommandLineTools/usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for ar... ar checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok 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... no checking for -exported_symbols_list linker flag... 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 (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... darwin22.6.0 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 for gcc... (cached) gcc checking whether we are using the GNU C compiler... (cached) yes checking whether gcc accepts -g... (cached) yes checking for gcc option to accept ISO C89... (cached) none needed checking dependency style of gcc... (cached) gcc3 checking how to run the C preprocessor... gcc -E 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 whether we are using the GNU C++ compiler... (cached) yes checking whether g++ accepts -g... (cached) yes checking dependency style of g++... (cached) gcc3 checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /Library/Developer/CommandLineTools/usr/bin/ld checking if the linker (/Library/Developer/CommandLineTools/usr/bin/ld) is GNU ld... no checking whether the g++ linker (/Library/Developer/CommandLineTools/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 (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... darwin22.6.0 dyld checking how to hardcode library paths into programs... immediate checking how to run the C++ preprocessor... g++ -E checking for ANSI C header files... (cached) yes checking assert.h usability... yes checking assert.h presence... yes checking for assert.h... yes checking ctype.h usability... yes checking ctype.h presence... yes checking for ctype.h... yes checking float.h usability... yes checking float.h presence... yes checking for float.h... yes checking limits.h usability... yes checking limits.h presence... yes checking for limits.h... yes checking math.h usability... yes checking math.h presence... yes checking for math.h... yes checking for memory.h... (cached) yes checking stdarg.h usability... yes checking stdarg.h presence... yes checking for stdarg.h... yes checking stdio.h usability... yes checking stdio.h presence... yes checking for stdio.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking time.h usability... yes checking time.h presence... yes checking for time.h... yes checking for unistd.h... (cached) yes checking for an ANSI C-conforming const... yes checking for size_t... yes checking for inline... inline checking for log in -lm... yes checking for log2 in -lm... yes checking whether byte ordering is bigendian... no checking for ntohs... yes checking for ntohl... yes checking for ntons... no checking for ntonl... no checking size of unsigned short... 2 checking size of unsigned int... 4 checking size of unsigned long... 8 checking size of unsigned long long... 8 checking for stroul... no checking for strtoull... yes checking for ftello... yes checking for fseeko... yes checking for ftello64... no checking for fseeko64... no checking for ftell64... no checking for fseek64... no checking for off_t... yes checking size of fpos_t... 8 checking if malloc debugging is wanted... no checking whether to build with debug information... no configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating clustalo.pc config.status: creating Doxyfile config.status: creating src/exceptions4c/Makefile config.status: creating src/clustal/Makefile config.status: creating src/hhalign/Makefile config.status: creating src/kmpp/Makefile config.status: creating src/squid/Makefile config.status: creating src/argtable2/Makefile config.status: creating src/config.h config.status: executing src/clustal-omega-config.h commands config.status: creating src/clustal-omega-config.h - prefix CLUSTAL_OMEGA for src/config.h defines config.status: src/clustal-omega-config.h is unchanged config.status: executing depfiles commands config.status: executing libtool commands using C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ 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'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -falign-functions=64 -Wall -g -O2 -c exceptions4c/e4c_lite.c -o exceptions4c/e4c_lite.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -falign-functions=64 -Wall -g -O2 -c argtable2/argtable2.c -o argtable2/argtable2.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -falign-functions=64 -Wall -g -O2 -c argtable2/arg_end.c -o argtable2/arg_end.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -falign-functions=64 -Wall -g -O2 -c argtable2/arg_rem.c -o argtable2/arg_rem.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -falign-functions=64 -Wall -g -O2 -c argtable2/arg_lit.c -o argtable2/arg_lit.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -falign-functions=64 -Wall -g -O2 -c argtable2/arg_int.c -o argtable2/arg_int.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -falign-functions=64 -Wall -g -O2 -c argtable2/arg_dbl.c -o argtable2/arg_dbl.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -falign-functions=64 -Wall -g -O2 -c argtable2/arg_str.c -o argtable2/arg_str.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -falign-functions=64 -Wall -g -O2 -c argtable2/arg_file.c -o argtable2/arg_file.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -DMATH_H_CLIB -std=c++11 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -falign-functions=64 -Wall -g -O2 -c kmpp/KMeans.cpp -o kmpp/KMeans.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -DMATH_H_CLIB -std=c++11 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -falign-functions=64 -Wall -g -O2 -c kmpp/KmTree.cpp -o kmpp/KmTree.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -DMATH_H_CLIB -std=c++11 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -falign-functions=64 -Wall -g -O2 -c kmpp/KmUtils.cpp -o kmpp/KmUtils.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -falign-functions=64 -Wall -g -O2 -c clustal/hhalign_wrapper.c -o clustal/hhalign_wrapper.o In file included from clustal/hhalign_wrapper.c:22: ./config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG /**/ ^ :1:9: note: previous definition is here #define NDEBUG 1 ^ clustal/hhalign_wrapper.c:84:9: warning: unused variable 'iR' [-Wunused-variable] int iR; /* iterator for residue */ ^ clustal/hhalign_wrapper.c:85:9: warning: unused variable 'iLen' [-Wunused-variable] int iLen; /* length of sequence */ ^ clustal/hhalign_wrapper.c:238:9: warning: variable 'iSize1' set but not used [-Wunused-but-set-variable] int iSize1 = 0; /* #seqs in 1st profile */ ^ clustal/hhalign_wrapper.c:239:9: warning: variable 'iSize2' set but not used [-Wunused-but-set-variable] int iSize2 = 0; /* #seqs in 2nd profile */ ^ 5 warnings generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -falign-functions=64 -Wall -g -O2 -c clustal/ktuple_pair.c -o clustal/ktuple_pair.o In file included from clustal/ktuple_pair.c:29: ./config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG /**/ ^ :1:9: note: previous definition is here #define NDEBUG 1 ^ clustal/ktuple_pair.c:640:9: warning: variable 'private_step_no' set but not used [-Wunused-but-set-variable] int private_step_no = 0; ^ 2 warnings generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -falign-functions=64 -Wall -g -O2 -c clustal/list.c -o clustal/list.o In file included from clustal/list.c:32: ./config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG /**/ ^ :1:9: note: previous definition is here #define NDEBUG 1 ^ 1 warning generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -falign-functions=64 -Wall -g -O2 -c clustal/log.c -o clustal/log.o In file included from clustal/log.c:22: ./config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG /**/ ^ :1:9: note: previous definition is here #define NDEBUG 1 ^ 1 warning generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -falign-functions=64 -Wall -g -O2 -c clustal/muscle_upgma.c -o clustal/muscle_upgma.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -falign-functions=64 -Wall -g -O2 -c clustal/muscle_tree.c -o clustal/muscle_tree.o clustal/muscle_tree.c:42:21: warning: unused variable 'VERY_NEGATIVE_DOUBLE' [-Wunused-const-variable] static const double VERY_NEGATIVE_DOUBLE = -9e29; ^ clustal/muscle_tree.c:519:1: warning: unused function 'IsEdge' [-Wunused-function] IsEdge(unsigned uNodeIndex1, unsigned uNodeIndex2, tree_t *tree) ^ 2 warnings generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -falign-functions=64 -Wall -g -O2 -c clustal/mbed.c -o clustal/mbed.o In file included from clustal/mbed.c:28: ./config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG /**/ ^ :1:9: note: previous definition is here #define NDEBUG 1 ^ clustal/mbed.c:786:16: warning: variable 'dCost' set but not used [-Wunused-but-set-variable] double dCost = -1.0; ^ clustal/mbed.c:69:18: warning: unused variable 'MAX_ALLOWED_SEQ_PER_PRECLUSTER' [-Wunused-const-variable] static const int MAX_ALLOWED_SEQ_PER_PRECLUSTER = 100; ^ 3 warnings generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -falign-functions=64 -Wall -g -O2 -c clustal/pair_dist.c -o clustal/pair_dist.o In file included from clustal/pair_dist.c:22: ./config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG /**/ ^ :1:9: note: previous definition is here #define NDEBUG 1 ^ clustal/pair_dist.c:177:10: warning: unused variable 'bPrintCR' [-Wunused-variable] bool bPrintCR = (rLog.iLogLevelEnabled<=LOG_VERBOSE) ? FALSE : TRUE; ^ 2 warnings generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -falign-functions=64 -Wall -g -O2 -c clustal/progress.c -o clustal/progress.o In file included from clustal/progress.c:22: ./config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG /**/ ^ :1:9: note: previous definition is here #define NDEBUG 1 ^ 1 warning generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -falign-functions=64 -Wall -g -O2 -c clustal/seq.c -o clustal/seq.o In file included from clustal/seq.c:30: ./config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG /**/ ^ :1:9: note: previous definition is here #define NDEBUG 1 ^ clustal/seq.c:68:9: warning: unused variable 'iAux' [-Wunused-variable] int iAux; ^ 2 warnings generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -falign-functions=64 -Wall -g -O2 -c clustal/symmatrix.c -o clustal/symmatrix.o In file included from clustal/symmatrix.c:30: ./config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG /**/ ^ :1:9: note: previous definition is here #define NDEBUG 1 ^ 1 warning generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -falign-functions=64 -Wall -g -O2 -c clustal/tree.c -o clustal/tree.o In file included from clustal/tree.c:22: ./config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG /**/ ^ :1:9: note: previous definition is here #define NDEBUG 1 ^ 1 warning generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -falign-functions=64 -Wall -g -O2 -c clustal/util.c -o clustal/util.o In file included from clustal/util.c:22: ./config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG /**/ ^ :1:9: note: previous definition is here #define NDEBUG 1 ^ 1 warning generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -falign-functions=64 -Wall -g -O2 -c clustal/weights.c -o clustal/weights.o In file included from clustal/weights.c:72: ./config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG /**/ ^ :1:9: note: previous definition is here #define NDEBUG 1 ^ 1 warning generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -falign-functions=64 -Wall -g -O2 -c squid/a2m.c -o squid/a2m.o In file included from squid/a2m.c:20: In file included from squid/squid.h:32: squid/../config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG /**/ ^ :1:9: note: previous definition is here #define NDEBUG 1 ^ 1 warning generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -falign-functions=64 -Wall -g -O2 -c squid/aligneval.c -o squid/aligneval.o In file included from squid/aligneval.c:59: In file included from squid/squid.h:32: squid/../config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG /**/ ^ :1:9: note: previous definition is here #define NDEBUG 1 ^ 1 warning generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -falign-functions=64 -Wall -g -O2 -c squid/alignio.c -o squid/alignio.o In file included from squid/alignio.c:21: In file included from squid/squid.h:32: squid/../config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG /**/ ^ :1:9: note: previous definition is here #define NDEBUG 1 ^ 1 warning generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -falign-functions=64 -Wall -g -O2 -c squid/clustal.c -o squid/clustal.o In file included from squid/clustal.c:24: In file included from squid/squid.h:32: squid/../config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG /**/ ^ :1:9: note: previous definition is here #define NDEBUG 1 ^ squid/clustal.c:214:7: warning: unused variable 'cons' [-Wunused-variable] int cons; ^ squid/clustal.c:438:6: warning: unused variable 'cons' [-Wunused-variable] int cons; ^ 3 warnings generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -falign-functions=64 -Wall -g -O2 -c squid/cluster.c -o squid/cluster.o In file included from squid/cluster.c:124: In file included from squid/squid.h:32: squid/../config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG /**/ ^ :1:9: note: previous definition is here #define NDEBUG 1 ^ 1 warning generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -falign-functions=64 -Wall -g -O2 -c squid/dayhoff.c -o squid/dayhoff.o In file included from squid/dayhoff.c:28: In file included from squid/squid.h:32: squid/../config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG /**/ ^ :1:9: note: previous definition is here #define NDEBUG 1 ^ 1 warning generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -falign-functions=64 -Wall -g -O2 -c squid/eps.c -o squid/eps.o In file included from squid/eps.c:23: In file included from squid/squid.h:32: squid/../config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG /**/ ^ :1:9: note: previous definition is here #define NDEBUG 1 ^ 1 warning generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -falign-functions=64 -Wall -g -O2 -c squid/file.c -o squid/file.o In file included from squid/file.c:28: In file included from squid/squid.h:32: squid/../config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG /**/ ^ :1:9: note: previous definition is here #define NDEBUG 1 ^ 1 warning generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -falign-functions=64 -Wall -g -O2 -c squid/getopt.c -o squid/getopt.o In file included from squid/getopt.c:17: In file included from squid/squid.h:32: squid/../config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG /**/ ^ :1:9: note: previous definition is here #define NDEBUG 1 ^ 1 warning generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -falign-functions=64 -Wall -g -O2 -c squid/gki.c -o squid/gki.o In file included from squid/gki.c:82: In file included from squid/squid.h:32: squid/../config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG /**/ ^ :1:9: note: previous definition is here #define NDEBUG 1 ^ 1 warning generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -falign-functions=64 -Wall -g -O2 -c squid/gsi.c -o squid/gsi.o In file included from squid/gsi.c:35: In file included from squid/squid.h:32: squid/../config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG /**/ ^ :1:9: note: previous definition is here #define NDEBUG 1 ^ 1 warning generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -falign-functions=64 -Wall -g -O2 -c squid/gsi64.c -o squid/gsi64.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -falign-functions=64 -Wall -g -O2 -c squid/hsregex.c -o squid/hsregex.o In file included from squid/hsregex.c:33: In file included from squid/squid.h:32: squid/../config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG /**/ ^ :1:9: note: previous definition is here #define NDEBUG 1 ^ squid/hsregex.c:333:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] sqd_regcomp(exp) ^ squid/hsregex.c:422:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] reg(cp, paren, flagp) ^ squid/hsregex.c:492:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] regbranch(cp, flagp) ^ squid/hsregex.c:533:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] regpiece(cp, flagp) ^ squid/hsregex.c:602:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] regatom(cp, flagp) ^ squid/hsregex.c:711:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] regnode(cp, op) ^ squid/hsregex.c:736:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] regc(cp, b) ^ squid/hsregex.c:752:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] reginsert(cp, op, opnd) ^ squid/hsregex.c:777:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] regtail(cp, p, val) ^ squid/hsregex.c:802:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] regoptail(cp, p, val) ^ squid/hsregex.c:844:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] sqd_regexec(prog, str) ^ squid/hsregex.c:898:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] regtry(ep, prog, string) ^ squid/hsregex.c:934:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] regmatch(ep, prog) ^ squid/hsregex.c:1089:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] regrepeat(ep, node) ^ squid/hsregex.c:1126:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] regnext(p) ^ squid/hsregex.c:1272:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] sqd_regsub(rp, source, dest) ^ squid/hsregex.c:1321:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] sqd_regerror(s) ^ 18 warnings generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -falign-functions=64 -Wall -g -O2 -c squid/iupac.c -o squid/iupac.o In file included from squid/iupac.c:17: In file included from squid/squid.h:32: squid/../config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG /**/ ^ :1:9: note: previous definition is here #define NDEBUG 1 ^ 1 warning generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -falign-functions=64 -Wall -g -O2 -c squid/msa.c -o squid/msa.o In file included from squid/msa.c:22: In file included from squid/squid.h:32: squid/../config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG /**/ ^ :1:9: note: previous definition is here #define NDEBUG 1 ^ 1 warning generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -falign-functions=64 -Wall -g -O2 -c squid/msf.c -o squid/msf.o In file included from squid/msf.c:25: In file included from squid/squid.h:32: squid/../config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG /**/ ^ :1:9: note: previous definition is here #define NDEBUG 1 ^ squid/msf.c:85:11: warning: variable 'alleged_alen' set but not used [-Wunused-but-set-variable] int alleged_alen; ^ squid/msf.c:87:11: warning: variable 'alleged_checksum' set but not used [-Wunused-but-set-variable] int alleged_checksum; ^ 3 warnings generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -falign-functions=64 -Wall -g -O2 -c squid/phylip.c -o squid/phylip.o In file included from squid/phylip.c:23: In file included from squid/squid.h:32: squid/../config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG /**/ ^ :1:9: note: previous definition is here #define NDEBUG 1 ^ squid/phylip.c:80:15: warning: variable 'alen' set but not used [-Wunused-but-set-variable] int nseq, alen; ^ 2 warnings generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -falign-functions=64 -Wall -g -O2 -c squid/revcomp.c -o squid/revcomp.o In file included from squid/revcomp.c:19: In file included from squid/squid.h:32: squid/../config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG /**/ ^ :1:9: note: previous definition is here #define NDEBUG 1 ^ 1 warning generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -falign-functions=64 -Wall -g -O2 -c squid/rk.c -o squid/rk.o In file included from squid/rk.c:26: In file included from squid/squid.h:32: squid/../config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG /**/ ^ :1:9: note: previous definition is here #define NDEBUG 1 ^ 1 warning generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -falign-functions=64 -Wall -g -O2 -c squid/selex.c -o squid/selex.o In file included from squid/selex.c:43: In file included from squid/squid.h:32: squid/../config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG /**/ ^ :1:9: note: previous definition is here #define NDEBUG 1 ^ 1 warning generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -falign-functions=64 -Wall -g -O2 -c squid/seqencode.c -o squid/seqencode.o In file included from squid/seqencode.c:18: In file included from squid/squid.h:32: squid/../config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG /**/ ^ :1:9: note: previous definition is here #define NDEBUG 1 ^ 1 warning generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -falign-functions=64 -Wall -g -O2 -c squid/shuffle.c -o squid/shuffle.o In file included from squid/shuffle.c:42: In file included from squid/squid.h:32: squid/../config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG /**/ ^ :1:9: note: previous definition is here #define NDEBUG 1 ^ 1 warning generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -falign-functions=64 -Wall -g -O2 -c squid/sqerror.c -o squid/sqerror.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -falign-functions=64 -Wall -g -O2 -c squid/sqio.c -o squid/sqio.o In file included from squid/sqio.c:57: In file included from squid/squid.h:32: squid/../config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG /**/ ^ :1:9: note: previous definition is here #define NDEBUG 1 ^ 1 warning generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -falign-functions=64 -Wall -g -O2 -c squid/squidcore.c -o squid/squidcore.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -falign-functions=64 -Wall -g -O2 -c squid/sre_ctype.c -o squid/sre_ctype.o In file included from squid/sre_ctype.c:19: In file included from squid/squid.h:32: squid/../config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG /**/ ^ :1:9: note: previous definition is here #define NDEBUG 1 ^ 1 warning generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -falign-functions=64 -Wall -g -O2 -c squid/sre_math.c -o squid/sre_math.o In file included from squid/sre_math.c:19: In file included from squid/squid.h:32: squid/../config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG /**/ ^ :1:9: note: previous definition is here #define NDEBUG 1 ^ 1 warning generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -falign-functions=64 -Wall -g -O2 -c squid/sre_random.c -o squid/sre_random.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -falign-functions=64 -Wall -g -O2 -c squid/sre_string.c -o squid/sre_string.o In file included from squid/sre_string.c:23: In file included from squid/squid.h:32: squid/../config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG /**/ ^ :1:9: note: previous definition is here #define NDEBUG 1 ^ 1 warning generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -falign-functions=64 -Wall -g -O2 -c squid/ssi.c -o squid/ssi.o In file included from squid/ssi.c:16: In file included from squid/squid.h:32: squid/../config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG /**/ ^ :1:9: note: previous definition is here #define NDEBUG 1 ^ 1 warning generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -falign-functions=64 -Wall -g -O2 -c squid/stack.c -o squid/stack.o In file included from squid/stack.c:18: In file included from squid/squid.h:32: squid/../config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG /**/ ^ :1:9: note: previous definition is here #define NDEBUG 1 ^ 1 warning generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -falign-functions=64 -Wall -g -O2 -c squid/stockholm.c -o squid/stockholm.o In file included from squid/stockholm.c:31: In file included from squid/squid.h:32: squid/../config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG /**/ ^ :1:9: note: previous definition is here #define NDEBUG 1 ^ 1 warning generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -falign-functions=64 -Wall -g -O2 -c squid/stopwatch.c -o squid/stopwatch.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -falign-functions=64 -Wall -g -O2 -c squid/translate.c -o squid/translate.o In file included from squid/translate.c:19: In file included from squid/squid.h:32: squid/../config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG /**/ ^ :1:9: note: previous definition is here #define NDEBUG 1 ^ 1 warning generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -falign-functions=64 -Wall -g -O2 -c squid/types.c -o squid/types.o In file included from squid/types.c:20: In file included from squid/squid.h:32: squid/../config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG /**/ ^ :1:9: note: previous definition is here #define NDEBUG 1 ^ 1 warning generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -falign-functions=64 -Wall -g -O2 -c squid/vectorops.c -o squid/vectorops.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -falign-functions=64 -Wall -g -O2 -c squid/weight.c -o squid/weight.o In file included from squid/weight.c:19: In file included from squid/squid.h:32: squid/../config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG /**/ ^ :1:9: note: previous definition is here #define NDEBUG 1 ^ 1 warning generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -DMATH_H_CLIB -std=c++11 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -falign-functions=64 -Wall -g -O2 -c hhalign/hhalign.cpp -o hhalign/hhalign.o In file included from hhalign/hhalign.cpp:82: hhalign/hhhmm-C.h:344:60: warning: while loop has empty body [-Wempty-body] {while (fgetline(line,LINELEN-1,dbf) && line[0]!='#'); break;} ^ hhalign/hhhmm-C.h:344:60: note: put the semicolon on a separate line to silence this warning hhalign/hhhmm-C.h:355:57: warning: while loop has empty body [-Wempty-body] {while (fgetline(line,LINELEN-1,dbf) && line[0]!='#'); k--; break;} ^ hhalign/hhhmm-C.h:355:57: note: put the semicolon on a separate line to silence this warning hhalign/hhhmm-C.h:1141:12: warning: variable 'dAlphaInv' set but not used [-Wunused-but-set-variable] double dAlphaInv = 1.00 / (double)(iAlpha); /* weight of AA */ ^ In file included from hhalign/hhalign.cpp:83: hhalign/hhalignment-C.h:134:33: warning: argument 'infile' of type 'char[]' with mismatched bound [-Warray-parameter] Alignment::Read(FILE* inf, char infile[], char* firstline) ^ hhalign/hhalignment.h:64:29: note: previously declared as 'char[511]' here void Read(FILE* inf, char infile[NAMELEN], char* line=NULL); ^ In file included from hhalign/hhalign.cpp:83: hhalign/hhalignment-C.h:245:32: warning: variable 'ptr2' set but not used [-Wunused-but-set-variable] char *ptr1, *ptr2; ^ hhalign/hhalignment-C.h:410:32: warning: argument 'infile' of type 'const char[]' with mismatched bound [-Warray-parameter] Alignment::Compress(const char infile[]) ^ hhalign/hhalignment.h:73:28: note: previously declared as 'const char[511]' here void Compress(const char infile[NAMELEN]); ^ In file included from hhalign/hhalign.cpp:83: hhalign/hhalignment-C.h:1429:19: warning: variable 'score_M' set but not used [-Wunused-but-set-variable] float score_M=0.0; ^ hhalign/hhalignment-C.h:1430:19: warning: variable 'score_prev' set but not used [-Wunused-but-set-variable] float score_prev=0.0; ^ hhalign/hhalignment-C.h:1908:43: warning: add explicit braces to avoid dangling else [-Wdangling-else] if(in[k] && X[k][i]0) wi[k]=wg[k]; else wi[k]=0.0; ^ hhalign/hhalignment-C.h:2347:76: warning: add explicit braces to avoid dangling else [-Wdangling-else] if(in[k] && X[k][i]==GAP) wi[k]=wg[k]; else wi[k]=0.0; ^ In file included from hhalign/hhalign.cpp:87: hhalign/hhhitlist-C.h:309:7: warning: variable 'i' set but not used [-Wunused-but-set-variable] int i=0, n; ^ hhalign/hhhitlist-C.h:663:9: warning: address of array 'q.fam' will always evaluate to 'true' [-Wpointer-bool-conversion] if (q.fam && q.fam[0]>='a' && q.fam[0]<='k' && q.fam[1]=='.') ~~^~~ ~~ hhalign/hhhitlist-C.h:840:9: warning: address of array 'q.fam' will always evaluate to 'true' [-Wpointer-bool-conversion] if (q.fam && q.fam[0]>='a' && q.fam[0]<='k' && q.fam[1]=='.') ~~^~~ ~~ hhalign/hhhitlist-C.h:1259:10: warning: variable 'unused' set but not used [-Wunused-but-set-variable] size_t unused; /* disable fread gcc warning */ ^ hhalign/hhhitlist-C.h:1624:10: warning: variable 'unused' set but not used [-Wunused-but-set-variable] size_t unused; /* disable fread gcc warning */ ^ hhalign/hhhitlist-C.h:1994:10: warning: variable 'unused' set but not used [-Wunused-but-set-variable] size_t unused; /* disable fread gcc warning */ ^ hhalign/hhhitlist-C.h:2359:10: warning: variable 'unused' set but not used [-Wunused-but-set-variable] size_t unused; /* disable fread gcc warning */ ^ In file included from hhalign/hhalign.cpp:88: hhalign/hhfunc-C.h:74:9: warning: unused variable 'iT' [-Wunused-variable] int iT; /* transition state iterator */ ^ hhalign/hhfunc-C.h:80:11: warning: unused variable 'fGThgiew' [-Wunused-variable] float fGThgiew = UNITY - fGWeight; /* weight of 'true' transitions */ ^ hhalign/hhfunc-C.h:85:11: warning: unused variable 'zf1SeqTrans' [-Wunused-variable] float zf1SeqTrans[] = {0.98, 0.01, 0.01, 0.25, 0.75, 0.25, 0.75}; ^ hhalign/hhfunc-C.h:86:11: warning: unused variable 'zf1SeqInit' [-Wunused-variable] float zf1SeqInit[] = {0.98, 0.01, 0.01, 0.99, 0.01, 0.99, 0.01}; ^ hhalign/hhfunc-C.h:87:11: warning: unused variable 'zf1SeqDel' [-Wunused-variable] float zf1SeqDel[] = {0.24, 0.01, 0.75, 0.01, 0.01, 0.01, 0.01}; ^ hhalign/hhfunc-C.h:88:11: warning: unused variable 'zf1SeqRevrt' [-Wunused-variable] float zf1SeqRevrt[] = {0.98, 0.01, 0.01, 0.01, 0.01, 0.99, 0.01}; ^ hhalign/hhfunc-C.h:328:17: warning: unused variable 'NEFF_SCORE' [-Wunused-variable] const int NEFF_SCORE = 10; /* FIXME: Magic Number */ ^ hhalign/hhfunc-C.h:511:17: warning: unused variable 'NEFF_SCORE' [-Wunused-variable] const int NEFF_SCORE = 10; /* FIXME: Magic Number */ ^ hhalign/hhalign.cpp:727:9: warning: variable 'Nali' set but not used [-Wunused-but-set-variable] int Nali; /* number of normally backtraced alignments ^ 27 warnings generated. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -DMATH_H_CLIB -std=c++11 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -falign-functions=64 -Wall -g -O2 -c RClustalOmega.cpp -o RClustalOmega.o In file included from RClustalOmega.cpp:27: ./config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG /**/ ^ :1:9: note: previous definition is here #define NDEBUG 1 ^ 1 warning generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -falign-functions=64 -Wall -g -O2 -c mymain.c -o mymain.o In file included from mymain.c:22: ./config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG /**/ ^ :1:9: note: previous definition is here #define NDEBUG 1 ^ 1 warning generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-8.2.2/include -fPIC -falign-functions=64 -Wall -g -O2 -c clustal-omega.c -o clustal-omega.o In file included from clustal-omega.c:22: ./config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined] #define NDEBUG /**/ ^ :1:9: note: previous definition is here #define NDEBUG 1 ^ clustal-omega.c:134:58: warning: implicit conversion from 'double' to 'int' changes value from 0.01 to 0 [-Wliteral-conversion] static const int ITERATION_SCORE_IMPROVEMENT_THRESHOLD = 0.01; ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^~~~ clustal-omega.c:134:18: warning: unused variable 'ITERATION_SCORE_IMPROVEMENT_THRESHOLD' [-Wunused-const-variable] static const int ITERATION_SCORE_IMPROVEMENT_THRESHOLD = 0.01; ^ 3 warnings generated. 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 libClustalOmega.so exceptions4c/e4c_lite.o argtable2/argtable2.o argtable2/arg_end.o argtable2/arg_rem.o argtable2/arg_lit.o argtable2/arg_int.o argtable2/arg_dbl.o argtable2/arg_str.o argtable2/arg_file.o kmpp/KMeans.o kmpp/KmTree.o kmpp/KmUtils.o clustal/hhalign_wrapper.o clustal/ktuple_pair.o clustal/list.o clustal/log.o clustal/muscle_upgma.o clustal/muscle_tree.o clustal/mbed.o clustal/pair_dist.o clustal/progress.o clustal/seq.o clustal/symmatrix.o clustal/tree.o clustal/util.o clustal/weights.o squid/a2m.o squid/aligneval.o squid/alignio.o squid/clustal.o squid/cluster.o squid/dayhoff.o squid/eps.o squid/file.o squid/getopt.o squid/gki.o squid/gsi.o squid/gsi64.o squid/hsregex.o squid/iupac.o squid/msa.o squid/msf.o squid/phylip.o squid/revcomp.o squid/rk.o squid/selex.o squid/seqencode.o squid/shuffle.o squid/sqerror.o squid/sqio.o squid/squidcore.o squid/sre_ctype.o squid/sre_math.o squid/sre_random.o squid/sre_string.o squid/ssi.o squid/stack.o squid/stockholm.o squid/stopwatch.o squid/translate.o squid/types.o squid/vectorops.o squid/weight.o hhalign/hhalign.o RClustalOmega.o mymain.o clustal-omega.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation ---------------------------------------- ------------- ClustalOmega ------------- ---------------------------------------- --------- Compilation finished --------- ---------------------------------------- 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 msa.so R_init_msa.o SplitCharVector2List.o SplitCharVector2Matrix.o -Wl,-all_load ./libgc.a ./libClustalW.a ./libClustalOmega.a ./libMuscle.a -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.19-bioc/meat/msa.buildbin-libdir/00LOCK-msa/00new/msa/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 (msa) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR msa.buildbin-libdir/msa/libs/msa.so >>>>>>> >>>>>>> Paths before fix: msa.buildbin-libdir/msa/libs/msa.so: msa.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.1) /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101) /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/4.4-arm64/Resources/lib/libgcc_s.1.1.dylib" "msa.buildbin-libdir/msa/libs/msa.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgfortran.5.dylib" "msa.buildbin-libdir/msa/libs/msa.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libquadmath.0.dylib" "msa.buildbin-libdir/msa/libs/msa.so" >>>>>>> Paths after fix: msa.buildbin-libdir/msa/libs/msa.so: msa.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.1) /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101) /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)