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This page was generated on 2024-02-20 11:38:03 -0500 (Tue, 20 Feb 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" 4690
palomino4Windows Server 2022 Datacenterx644.3.2 (2023-10-31 ucrt) -- "Eye Holes" 4443
lconwaymacOS 12.7.1 Montereyx86_644.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" 4464
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1320/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
msa 1.34.0  (landing page)
Ulrich Bodenhofer
Snapshot Date: 2024-02-19 14:05:07 -0500 (Mon, 19 Feb 2024)
git_url: https://git.bioconductor.org/packages/msa
git_branch: RELEASE_3_18
git_last_commit: 2df795c
git_last_commit_date: 2023-10-24 10:43:22 -0500 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

BUILD BIN results for msa on lconway


To the developers/maintainers of the msa package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/msa.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: msa
Version: 1.34.0
Command: rm -rf msa.buildbin-libdir && mkdir msa.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh msa_1.34.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R msa.buildbin-libdir
StartedAt: 2024-02-20 00:33:35 -0500 (Tue, 20 Feb 2024)
EndedAt: 2024-02-20 00:42:10 -0500 (Tue, 20 Feb 2024)
EllapsedTime: 514.6 seconds
RetCode: 0
Status:   OK  
PackageFile: msa_1.34.0.tgz
PackageFileSize: 1.871 MiB

Command output

##############################################################################
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###
### Running command:
###
###   rm -rf msa.buildbin-libdir && mkdir msa.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh msa_1.34.0.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_1.34.0.tar.gz'
>>>>>>> 

* installing *source* package ‘msa’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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... x86_64-apple-darwin21.6.0
checking host system type... x86_64-apple-darwin21.6.0
checking target system type... x86_64-apple-darwin21.6.0
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 x86_64-apple-darwin21.6.0 file names to x86_64-apple-darwin21.6.0 format... func_convert_file_noop
checking how to convert x86_64-apple-darwin21.6.0 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... yes
checking for -exported_symbols_list linker flag... yes
checking for -force_load linker flag... yes
checking how to run the C preprocessor... gcc -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for dlfcn.h... yes
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... yes
checking for gcc option to produce PIC... -fno-common -DPIC
checking if gcc PIC flag -fno-common -DPIC works... yes
checking if gcc static flag -static works... no
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... darwin21.6.0 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... darwin21.6.0 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... yes
checking for dladdr... yes
checking for sigsetjmp... yes
checking for pthread_setname_np... yes (w/o tid)
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 -Wno-frame-address  -MT allchblk.lo -MD -MP -MF $depbase.Tpo -c -o allchblk.lo allchblk.c &&\
	mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -Wall -Wextra -Wpedantic -Wno-long-long -g -O2 -fno-strict-aliasing -Wno-frame-address -MT allchblk.lo -MD -MP -MF .deps/allchblk.Tpo -c allchblk.c  -fno-common -DPIC -o allchblk.o
depbase=`echo alloc.lo | sed 's|[^/]*$|.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 -Wno-frame-address  -MT alloc.lo -MD -MP -MF $depbase.Tpo -c -o alloc.lo alloc.c &&\
	mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -Wall -Wextra -Wpedantic -Wno-long-long -g -O2 -fno-strict-aliasing -Wno-frame-address -MT alloc.lo -MD -MP -MF .deps/alloc.Tpo -c alloc.c  -fno-common -DPIC -o alloc.o
depbase=`echo blacklst.lo | sed 's|[^/]*$|.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 -Wno-frame-address  -MT blacklst.lo -MD -MP -MF $depbase.Tpo -c -o blacklst.lo blacklst.c &&\
	mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -Wall -Wextra -Wpedantic -Wno-long-long -g -O2 -fno-strict-aliasing -Wno-frame-address -MT blacklst.lo -MD -MP -MF .deps/blacklst.Tpo -c blacklst.c  -fno-common -DPIC -o blacklst.o
depbase=`echo dbg_mlc.lo | sed 's|[^/]*$|.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 -Wno-frame-address  -MT dbg_mlc.lo -MD -MP -MF $depbase.Tpo -c -o dbg_mlc.lo dbg_mlc.c &&\
	mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -Wall -Wextra -Wpedantic -Wno-long-long -g -O2 -fno-strict-aliasing -Wno-frame-address -MT dbg_mlc.lo -MD -MP -MF .deps/dbg_mlc.Tpo -c dbg_mlc.c  -fno-common -DPIC -o dbg_mlc.o
depbase=`echo dyn_load.lo | sed 's|[^/]*$|.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 -Wno-frame-address  -MT dyn_load.lo -MD -MP -MF $depbase.Tpo -c -o dyn_load.lo dyn_load.c &&\
	mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -Wall -Wextra -Wpedantic -Wno-long-long -g -O2 -fno-strict-aliasing -Wno-frame-address -MT dyn_load.lo -MD -MP -MF .deps/dyn_load.Tpo -c dyn_load.c  -fno-common -DPIC -o dyn_load.o
dyn_load.c:1497:12: warning: '_dyld_bind_fully_image_containing_address' is deprecated: first deprecated in macOS 10.5 - dlopen(RTLD_NOW) [-Wdeprecated-declarations]
      if (!_dyld_bind_fully_image_containing_address(
           ^
/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/mach-o/dyld.h:259:13: note: '_dyld_bind_fully_image_containing_address' has been explicitly marked deprecated here
extern bool _dyld_bind_fully_image_containing_address(const void* address)                   __API_UNAVAILABLE(ios, tvos, watchos)  DYLD_DRIVERKIT_UNAVAILABLE  __OSX_DEPRECATED(10.1, 10.5, "dlopen(RTLD_NOW)");
            ^
1 warning generated.
depbase=`echo finalize.lo | sed 's|[^/]*$|.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 -Wno-frame-address  -MT finalize.lo -MD -MP -MF $depbase.Tpo -c -o finalize.lo finalize.c &&\
	mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -Wall -Wextra -Wpedantic -Wno-long-long -g -O2 -fno-strict-aliasing -Wno-frame-address -MT finalize.lo -MD -MP -MF .deps/finalize.Tpo -c finalize.c  -fno-common -DPIC -o finalize.o
depbase=`echo gc_dlopen.lo | sed 's|[^/]*$|.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 -Wno-frame-address  -MT gc_dlopen.lo -MD -MP -MF $depbase.Tpo -c -o gc_dlopen.lo gc_dlopen.c &&\
	mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -Wall -Wextra -Wpedantic -Wno-long-long -g -O2 -fno-strict-aliasing -Wno-frame-address -MT gc_dlopen.lo -MD -MP -MF .deps/gc_dlopen.Tpo -c gc_dlopen.c  -fno-common -DPIC -o gc_dlopen.o
depbase=`echo headers.lo | sed 's|[^/]*$|.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 -Wno-frame-address  -MT headers.lo -MD -MP -MF $depbase.Tpo -c -o headers.lo headers.c &&\
	mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -Wall -Wextra -Wpedantic -Wno-long-long -g -O2 -fno-strict-aliasing -Wno-frame-address -MT headers.lo -MD -MP -MF .deps/headers.Tpo -c headers.c  -fno-common -DPIC -o headers.o
depbase=`echo mach_dep.lo | sed 's|[^/]*$|.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 -Wno-frame-address  -MT mach_dep.lo -MD -MP -MF $depbase.Tpo -c -o mach_dep.lo mach_dep.c &&\
	mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -Wall -Wextra -Wpedantic -Wno-long-long -g -O2 -fno-strict-aliasing -Wno-frame-address -MT mach_dep.lo -MD -MP -MF .deps/mach_dep.Tpo -c mach_dep.c  -fno-common -DPIC -o mach_dep.o
depbase=`echo malloc.lo | sed 's|[^/]*$|.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 -Wno-frame-address  -MT malloc.lo -MD -MP -MF $depbase.Tpo -c -o malloc.lo malloc.c &&\
	mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -Wall -Wextra -Wpedantic -Wno-long-long -g -O2 -fno-strict-aliasing -Wno-frame-address -MT malloc.lo -MD -MP -MF .deps/malloc.Tpo -c malloc.c  -fno-common -DPIC -o malloc.o
depbase=`echo mallocx.lo | sed 's|[^/]*$|.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 -Wno-frame-address  -MT mallocx.lo -MD -MP -MF $depbase.Tpo -c -o mallocx.lo mallocx.c &&\
	mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -Wall -Wextra -Wpedantic -Wno-long-long -g -O2 -fno-strict-aliasing -Wno-frame-address -MT mallocx.lo -MD -MP -MF .deps/mallocx.Tpo -c mallocx.c  -fno-common -DPIC -o mallocx.o
depbase=`echo mark.lo | sed 's|[^/]*$|.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 -Wno-frame-address  -MT mark.lo -MD -MP -MF $depbase.Tpo -c -o mark.lo mark.c &&\
	mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -Wall -Wextra -Wpedantic -Wno-long-long -g -O2 -fno-strict-aliasing -Wno-frame-address -MT mark.lo -MD -MP -MF .deps/mark.Tpo -c mark.c  -fno-common -DPIC -o mark.o
depbase=`echo mark_rts.lo | sed 's|[^/]*$|.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 -Wno-frame-address  -MT mark_rts.lo -MD -MP -MF $depbase.Tpo -c -o mark_rts.lo mark_rts.c &&\
	mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -Wall -Wextra -Wpedantic -Wno-long-long -g -O2 -fno-strict-aliasing -Wno-frame-address -MT mark_rts.lo -MD -MP -MF .deps/mark_rts.Tpo -c mark_rts.c  -fno-common -DPIC -o mark_rts.o
depbase=`echo misc.lo | sed 's|[^/]*$|.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 -Wno-frame-address  -MT misc.lo -MD -MP -MF $depbase.Tpo -c -o misc.lo misc.c &&\
	mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -fexceptions -Wall -Wextra -Wpedantic -Wno-long-long -g -O2 -fno-strict-aliasing -Wno-frame-address -MT misc.lo -MD -MP -MF .deps/misc.Tpo -c misc.c  -fno-common -DPIC -o misc.o
depbase=`echo new_hblk.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
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/Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libgc.a(gc_dlopen.o) has no symbols
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/Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libgc.a(gc_dlopen.o) has no symbols
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/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
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/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 
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/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 -Wno-frame-address  -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
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/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 -Wno-frame-address  -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 -Wno-frame-address -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
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/bin/sh ./libtool  --tag=CC   --mode=link gcc   -fexceptions -Wall -Wextra -Wpedantic -Wno-long-long -g -O2 -fno-strict-aliasing -Wno-frame-address  -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 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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:187:17: warning: unused variable 'uLengthB' [-Wunused-variable]
        const unsigned uLengthB = msaB.GetColCount();
                       ^
aligngivenpath.cpp:186:17: warning: unused variable 'uLengthA' [-Wunused-variable]
        const unsigned uLengthA = msaA.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;
                                       ^
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)
              ^
8 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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:59:17: warning: unused variable 'uLengthB' [-Wunused-variable]
        const unsigned uLengthB = msaB.GetColCount();
                       ^
aligngivenpathsw.cpp:58:17: warning: unused variable 'uLengthA' [-Wunused-variable]
        const unsigned uLengthA = msaA.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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        {                                                                                             }
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)
           ^
26 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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:77:17: warning: unused variable 'uColCount' [-Wunused-variable]
        const unsigned uColCount = msa.GetColCount();
                       ^
diffobjscore.cpp:76:17: warning: unused variable 'uSeqCount' [-Wunused-variable]
        const unsigned uSeqCount = msa.GetSeqCount();
                       ^
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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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();
                       ^
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)
              ^
3 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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,
                        ^~~~~~~~~~~
<scratch space>:196:1: 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,
                        ^~~~~~~~~~~
<scratch space>:199:1: 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,
                        ^~~~~~~~~~~
<scratch space>:202:1: 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,
                        ^~~~~~~~~~~
<scratch space>:206:1: 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,
                        ^~~~~~~~~~~
<scratch space>:209:1: 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,
                        ^~~~~~~~~~~
<scratch space>:212:1: 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,
                        ^~~~~~~~~~~
<scratch space>:215:1: 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,
                        ^~~~~~~~~~~
<scratch space>:219:1: 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,
                        ^~~~~~~~~~~
<scratch space>:222:1: 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,
                        ^~~~~~~~~~~
<scratch space>:225:1: 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,
                        ^~~~~~~~~~~
<scratch space>:229:1: 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,
                        ^~~~~~~~~~~
<scratch space>:232:1: 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,
                        ^~~~~~~~~~~
<scratch space>:235:1: 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,
                        ^~~~~~~~~~~
<scratch space>:238:1: 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,
                        ^~~~~~~~~~~
<scratch space>:241:1: 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,
                        ^~~~~~~~~~~
<scratch space>:245:1: 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,
                        ^~~~~~~~~~~
<scratch space>:248:1: 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,
                        ^~~~~~~~~~~
<scratch space>:252:1: 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,
                        ^~~~~~~~~~~
<scratch space>:255:1: 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,
                        ^~~~~~~~~~~
<scratch space>:258:1: 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,
                        ^~~~~~~~~~~
<scratch space>:261:1: 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,
                        ^~~~~~~~~~~
<scratch space>:264:1: 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,
                        ^~~~~~~~~~~
<scratch space>:268:1: 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,
                        ^~~~~~~~~~~
<scratch space>:271:1: 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,
                        ^~~~~~~~~~~
<scratch space>:274:1: 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,
                        ^~~~~~~~~~~
<scratch space>:277:1: 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,
                        ^~~~~~~~~~~
<scratch space>:280:1: 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,
                        ^~~~~~~~~~~
<scratch space>:283:1: 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,
                        ^~~~~~~~~~~
<scratch space>:286:1: 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,
                        ^~~~~~~~~~~
<scratch space>:289:1: 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,
                        ^~~~~~~~~~~
<scratch space>:292:1: 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,
                        ^~~~~~~~~~~
<scratch space>:295:1: 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,
                        ^~~~~~~~~~~
<scratch space>:298:1: 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,
                        ^~~~~~~~~~~
<scratch space>:302:1: 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,
                        ^~~~~~~~~~~
<scratch space>:305:1: 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,
                        ^~~~~~~~~~~
<scratch space>:308:1: 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,
                        ^~~~~~~~~~~
<scratch space>:311:1: 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,
                        ^~~~~~~~~~~
<scratch space>:315:1: 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,
                        ^~~~~~~~~~~
<scratch space>:318:1: 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,
                        ^~~~~~~~~~~
<scratch space>:321:1: 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,
                        ^~~~~~~~~~~
<scratch space>:324:1: 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,
                        ^~~~~~~~~~~
<scratch space>:327:1: 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,
                        ^~~~~~~~~~~
<scratch space>:330:1: 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,
                        ^~~~~~~~~~~
<scratch space>:3:1: 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,
                        ^~~~~~~~~~~
<scratch space>:6:1: 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,
                        ^~~~~~~~~~~
<scratch space>:9:1: 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,
                        ^~~~~~~~~~~
<scratch space>:12:1: 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,
                        ^~~~~~~~~~~
<scratch space>:15:1: 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,
                        ^~~~~~~~~~~
<scratch space>:18:1: 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,
                        ^~~~~~~~~~~
<scratch space>:22:1: 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,
                        ^~~~~~~~~~~
<scratch space>:25:1: 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,
                        ^~~~~~~~~~~
<scratch space>:28:1: 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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c globalsosx.cpp -o globalsosx.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c globalswin32.cpp -o globalswin32.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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)
        ^
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)
              ^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c nwrec.cpp -o nwrec.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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:82:7: warning: variable 'bRightTermGap' set but not used [-Wunused-but-set-variable]
        bool bRightTermGap = 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:63:7: warning: unused variable 'bGapping1' [-Wunused-variable]
        bool bGapping1 = 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: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)
              ^
12 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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:190:9: warning: unused variable 'dAllMaxDist' [-Wunused-variable]
        double dAllMaxDist = -1e20;
               ^
phy3.cpp:192:11: warning: unused variable 'uMaxTo' [-Wunused-variable]
        unsigned uMaxTo = NULL_NEIGHBOR;
                 ^
phy3.cpp:191:11: warning: unused variable 'uMaxFrom' [-Wunused-variable]
        unsigned uMaxFrom = NULL_NEIGHBOR;
                 ^
phy3.cpp:167:17: warning: unused variable 'uLeafCount' [-Wunused-variable]
        const unsigned uLeafCount = tree.GetLeafCount();
                       ^
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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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:253:11: warning: unused variable 'uHydrophobicRunLength' [-Wunused-variable]
        unsigned uHydrophobicRunLength = 0;
                 ^
profilefrommsa.cpp:245:17: warning: unused variable 'uSeqCount' [-Wunused-variable]
        const unsigned uSeqCount = a.GetSeqCount();
                       ^
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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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: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)
              ^
4 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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:29:8: warning: unused variable 'scoreMax' [-Wunused-variable]
        SCORE scoreMax = DPM(uPrefixLengthA, uPrefixLengthB);
              ^
tracebacksw.cpp:22:17: warning: unused variable 'uPrefixCountB' [-Wunused-variable]
        const unsigned uPrefixCountB = uLengthB + 1;
                       ^
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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/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
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: libMuscle.a(blosumla.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: libMuscle.a(glbalign352.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: libMuscle.a(globalslinux.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: libMuscle.a(globalsother.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: libMuscle.a(globalswin32.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: libMuscle.a(nwdasimple2.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: libMuscle.a(nwdasmall.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: libMuscle.a(nwrec.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: libMuscle.a(objscoreda.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: libMuscle.a(pam200mafft.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: libMuscle.a(validateids.o) has no symbols
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... x86_64-apple-darwin21.6.0
checking host system type... x86_64-apple-darwin21.6.0
checking target system type... x86_64-apple-darwin21.6.0
building for darwin21.6.0
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 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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();
               ^
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/../substitutionMatrix/../general/userparams.h:8:
In file included from pairwise/../alignment/../general/UserParameters.h:22:
In file included from pairwise/../alignment/../substitutionMatrix/../general/utils.h:8:
In file included from pairwise/../alignment/../general/Utility.h:15:
In file included from pairwise/../alignment/../substitutionMatrix/../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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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/../substitutionMatrix/../general/userparams.h:8:
In file included from pairwise/../alignment/../general/UserParameters.h:22:
In file included from pairwise/../alignment/../substitutionMatrix/../general/utils.h:8:
In file included from pairwise/../alignment/../general/Utility.h:15:
In file included from pairwise/../alignment/../substitutionMatrix/../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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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/../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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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/../general/userparams.h:8:
In file included from fileInput/../alignment/../general/UserParameters.h:22:
In file included from fileInput/../general/utils.h:8:
In file included from fileInput/../alignment/../general/Utility.h:15:
In file included from fileInput/../alignment/../substitutionMatrix/../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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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/../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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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/../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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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/../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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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/../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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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/../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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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/../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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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/../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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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/../../general/userparams.h:8:
In file included from tree/UPGMA/../../alignment/../general/UserParameters.h:22:
In file included from tree/UPGMA/../../alignment/../substitutionMatrix/../general/utils.h:8:
In file included from tree/UPGMA/../../alignment/../general/Utility.h:15:
In file included from tree/UPGMA/../../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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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/../../alignment/../substitutionMatrix/../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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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/../../general/userparams.h:8:
In file included from tree/UPGMA/../../alignment/../general/UserParameters.h:22:
In file included from tree/UPGMA/../../alignment/../substitutionMatrix/../general/utils.h:8:
In file included from tree/UPGMA/../../alignment/../general/Utility.h:15:
In file included from tree/UPGMA/../../alignment/../substitutionMatrix/../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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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/../substitutionMatrix/../general/userparams.h:8:
In file included from tree/UPGMA/../../alignment/../general/UserParameters.h:22:
In file included from tree/UPGMA/../../alignment/../substitutionMatrix/../general/utils.h:8:
In file included from tree/UPGMA/../../alignment/../general/Utility.h:15:
In file included from tree/UPGMA/../../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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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/../substitutionMatrix/../general/userparams.h:8:
In file included from tree/../alignment/../general/UserParameters.h:22:
In file included from tree/../alignment/../substitutionMatrix/../general/utils.h:8:
In file included from tree/../alignment/../general/Utility.h:15:
In file included from tree/../alignment/../substitutionMatrix/../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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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:580:17: warning: variable 'rl' set but not used [-Wunused-but-set-variable]
    int rs = 0, rl = 0;
                ^
tree/ClusterTree.cpp:580:9: warning: variable 'rs' 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/../general/userparams.h:8:
In file included from tree/../alignment/../general/UserParameters.h:22:
In file included from tree/../general/utils.h:8:
In file included from tree/../alignment/../general/Utility.h:15:
In file included from tree/../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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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/UPGMA/../../alignment/Alignment.h:41:
In file included from tree/../alignment/Sequence.h:20:
In file included from tree/../general/userparams.h:8:
In file included from tree/../alignment/../general/UserParameters.h:22:
In file included from tree/../alignment/../substitutionMatrix/../general/utils.h:8:
In file included from tree/../alignment/../general/Utility.h:15:
In file included from tree/../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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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/../general/userparams.h:8:
In file included from tree/../alignment/../general/UserParameters.h:22:
In file included from tree/../general/utils.h:8:
In file included from tree/../alignment/../general/Utility.h:15:
In file included from tree/../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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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/../substitutionMatrix/../general/userparams.h:8:
In file included from tree/../alignment/../general/UserParameters.h:22:
In file included from tree/../alignment/../substitutionMatrix/../general/utils.h:8:
In file included from tree/../alignment/../general/Utility.h:15:
In file included from tree/../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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 interface/../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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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:697:9: warning: variable 'av1' set but not used [-Wunused-but-set-variable]
    int av1, av2, av3, min, max;  
        ^
substitutionMatrix/SubMatrix.cpp:1308:20: warning: unused variable 'ulimit' [-Wunused-variable]
    int n, llimit, ulimit;
                   ^
substitutionMatrix/SubMatrix.cpp:1305:10: warning: unused variable 'inline1' [-Wunused-variable]
    char inline1[1024];
         ^
substitutionMatrix/SubMatrix.cpp:1308:12: warning: unused variable 'llimit' [-Wunused-variable]
    int n, llimit, ulimit;
           ^
substitutionMatrix/SubMatrix.cpp:1308:9: warning: unused variable 'n' [-Wunused-variable]
    int n, llimit, ulimit;
        ^
substitutionMatrix/SubMatrix.cpp:1307:9: warning: unused variable 'nmat' [-Wunused-variable]
    int nmat;
        ^
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;
            ^
11 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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/../tree/../alignment/Alignment.h:41:
In file included from multipleAlign/../alignment/Sequence.h:20:
In file included from multipleAlign/../general/userparams.h:8:
In file included from multipleAlign/../alignment/../general/UserParameters.h:22:
In file included from multipleAlign/../general/utils.h:8:
In file included from multipleAlign/../alignment/../general/Utility.h:15:
In file included from multipleAlign/../tree/../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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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
          ^
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/../substitutionMatrix/../general/userparams.h:8:
In file included from multipleAlign/../alignment/../general/UserParameters.h:22:
In file included from multipleAlign/../alignment/../substitutionMatrix/../general/utils.h:8:
In file included from multipleAlign/../alignment/../general/Utility.h:15:
In file included from multipleAlign/../alignment/../substitutionMatrix/../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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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/../substitutionMatrix/../general/userparams.h:8:
In file included from multipleAlign/../alignment/../general/UserParameters.h:22:
In file included from multipleAlign/../alignment/../substitutionMatrix/../general/utils.h:8:
In file included from multipleAlign/../alignment/../general/Utility.h:15:
In file included from multipleAlign/../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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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/../substitutionMatrix/../general/userparams.h:8:
In file included from multipleAlign/../alignment/../general/UserParameters.h:22:
In file included from multipleAlign/../alignment/../substitutionMatrix/../general/utils.h:8:
In file included from multipleAlign/../alignment/../general/Utility.h:15:
In file included from multipleAlign/../alignment/../substitutionMatrix/../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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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/../substitutionMatrix/../general/userparams.h:8:
In file included from multipleAlign/../alignment/../general/UserParameters.h:22:
In file included from multipleAlign/../alignment/../substitutionMatrix/../general/utils.h:8:
In file included from multipleAlign/../alignment/../general/Utility.h:15:
In file included from multipleAlign/../alignment/../substitutionMatrix/../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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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/../substitutionMatrix/../general/userparams.h:8:
In file included from multipleAlign/../alignment/../general/UserParameters.h:22:
In file included from multipleAlign/../alignment/../substitutionMatrix/../general/utils.h:8:
In file included from multipleAlign/../alignment/../general/Utility.h:15:
In file included from multipleAlign/../alignment/../substitutionMatrix/../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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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/../substitutionMatrix/../general/userparams.h:8:
In file included from multipleAlign/../alignment/../general/UserParameters.h:22:
In file included from multipleAlign/../alignment/../substitutionMatrix/../general/utils.h:8:
In file included from multipleAlign/../alignment/../general/Utility.h:15:
In file included from multipleAlign/../alignment/../substitutionMatrix/../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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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/../substitutionMatrix/../general/userparams.h:8:
In file included from general/UserParameters.h:22:
In file included from general/../alignment/../substitutionMatrix/../general/utils.h:8:
In file included from general/Utility.h:15:
In file included from general/../alignment/../substitutionMatrix/../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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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: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/../substitutionMatrix/../general/userparams.h:8:
In file included from alignment/../general/UserParameters.h:22:
In file included from alignment/../substitutionMatrix/../general/utils.h:8:
In file included from alignment/../general/Utility.h:15:
In file included from alignment/../substitutionMatrix/../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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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();
               ^
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/../substitutionMatrix/../general/userparams.h:8:
In file included from alignment/../general/UserParameters.h:22:
In file included from alignment/../substitutionMatrix/../general/utils.h:8:
In file included from alignment/../general/Utility.h:15:
In file included from alignment/../substitutionMatrix/../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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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/../substitutionMatrix/../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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 ./fileInput/../alignment/../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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 ./fileInput/../alignment/Alignment.h:41:
In file included from ./fileInput/../alignment/Sequence.h:20:
In file included from ./interface/../general/userparams.h:8:
In file included from ./general/UserParameters.h:22:
In file included from ./interface/../general/utils.h:8:
In file included from ./general/Utility.h:15:
In file included from ./interface/../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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/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
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: libClustalW.a(InvalidCombination.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: libClustalW.a(SymMatrix.o) has no symbols
----------------------------------------
--------------- 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++98 -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
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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 14.0.0 (clang-1400.0.29.202)’
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include     -DMATH_H_CLIB -std=c++98 -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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include     -DMATH_H_CLIB -std=c++98 -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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include     -DMATH_H_CLIB -std=c++98 -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 x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 /**/
        ^
<command line>: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:239:9: warning: variable 'iSize2' set but not used [-Wunused-but-set-variable]
    int iSize2 = 0; /* #seqs in 2nd profile */
        ^
clustal/hhalign_wrapper.c:238:9: warning: variable 'iSize1' set but not used [-Wunused-but-set-variable]
    int iSize1 = 0; /* #seqs in 1st profile */
        ^
5 warnings generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 /**/
        ^
<command line>:1:9: note: previous definition is here
#define NDEBUG 1
        ^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 /**/
        ^
<command line>:1:9: note: previous definition is here
#define NDEBUG 1
        ^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 /**/
        ^
<command line>:1:9: note: previous definition is here
#define NDEBUG 1
        ^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 /**/
        ^
<command line>: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 x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 /**/
        ^
<command line>: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 x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 /**/
        ^
<command line>:1:9: note: previous definition is here
#define NDEBUG 1
        ^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 /**/
        ^
<command line>: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 x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 /**/
        ^
<command line>:1:9: note: previous definition is here
#define NDEBUG 1
        ^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 /**/
        ^
<command line>:1:9: note: previous definition is here
#define NDEBUG 1
        ^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 /**/
        ^
<command line>:1:9: note: previous definition is here
#define NDEBUG 1
        ^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 /**/
        ^
<command line>:1:9: note: previous definition is here
#define NDEBUG 1
        ^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 /**/
        ^
<command line>:1:9: note: previous definition is here
#define NDEBUG 1
        ^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 /**/
        ^
<command line>:1:9: note: previous definition is here
#define NDEBUG 1
        ^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 /**/
        ^
<command line>:1:9: note: previous definition is here
#define NDEBUG 1
        ^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 /**/
        ^
<command line>: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 x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 /**/
        ^
<command line>:1:9: note: previous definition is here
#define NDEBUG 1
        ^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 /**/
        ^
<command line>:1:9: note: previous definition is here
#define NDEBUG 1
        ^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 /**/
        ^
<command line>:1:9: note: previous definition is here
#define NDEBUG 1
        ^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 /**/
        ^
<command line>:1:9: note: previous definition is here
#define NDEBUG 1
        ^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 /**/
        ^
<command line>:1:9: note: previous definition is here
#define NDEBUG 1
        ^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 /**/
        ^
<command line>:1:9: note: previous definition is here
#define NDEBUG 1
        ^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 /**/
        ^
<command line>:1:9: note: previous definition is here
#define NDEBUG 1
        ^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 /**/
        ^
<command line>:1:9: note: previous definition is here
#define NDEBUG 1
        ^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 /**/
        ^
<command line>:1:9: note: previous definition is here
#define NDEBUG 1
        ^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 /**/
        ^
<command line>:1:9: note: previous definition is here
#define NDEBUG 1
        ^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 /**/
        ^
<command line>: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 x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 /**/
        ^
<command line>: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 x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 /**/
        ^
<command line>:1:9: note: previous definition is here
#define NDEBUG 1
        ^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 /**/
        ^
<command line>:1:9: note: previous definition is here
#define NDEBUG 1
        ^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 /**/
        ^
<command line>:1:9: note: previous definition is here
#define NDEBUG 1
        ^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 /**/
        ^
<command line>:1:9: note: previous definition is here
#define NDEBUG 1
        ^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 /**/
        ^
<command line>:1:9: note: previous definition is here
#define NDEBUG 1
        ^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 /**/
        ^
<command line>:1:9: note: previous definition is here
#define NDEBUG 1
        ^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 /**/
        ^
<command line>:1:9: note: previous definition is here
#define NDEBUG 1
        ^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 /**/
        ^
<command line>:1:9: note: previous definition is here
#define NDEBUG 1
        ^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 /**/
        ^
<command line>:1:9: note: previous definition is here
#define NDEBUG 1
        ^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 /**/
        ^
<command line>:1:9: note: previous definition is here
#define NDEBUG 1
        ^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 /**/
        ^
<command line>:1:9: note: previous definition is here
#define NDEBUG 1
        ^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 /**/
        ^
<command line>:1:9: note: previous definition is here
#define NDEBUG 1
        ^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 /**/
        ^
<command line>:1:9: note: previous definition is here
#define NDEBUG 1
        ^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 /**/
        ^
<command line>:1:9: note: previous definition is here
#define NDEBUG 1
        ^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 /**/
        ^
<command line>:1:9: note: previous definition is here
#define NDEBUG 1
        ^
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include     -DMATH_H_CLIB -std=c++98 -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:76:
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:77:
hhalign/hhalignment-C.h:245:32: warning: variable 'ptr2' set but not used [-Wunused-but-set-variable]
                  char *ptr1, *ptr2;
                               ^
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]<ANY) wi[k]=wg[k]; else wi[k]=0.0;
                                                        ^
hhalign/hhalignment-C.h:2140:69: warning: add explicit braces to avoid dangling else [-Wdangling-else]
                                if(in[k] && I[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:81:
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:82:
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:721:9: warning: variable 'Nali' set but not used [-Wunused-but-set-variable]
    int Nali;                    /* number of normally backtraced alignments 
        ^
24 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include     -DMATH_H_CLIB -std=c++98 -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 /**/
        ^
<command line>:1:9: note: previous definition is here
#define NDEBUG 1
        ^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 /**/
        ^
<command line>:1:9: note: previous definition is here
#define NDEBUG 1
        ^
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/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 /**/
        ^
<command line>: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 x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/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
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: libClustalOmega.a(gsi64.o) has no symbols
----------------------------------------
------------- ClustalOmega -------------
----------------------------------------
--------- Compilation finished ---------
----------------------------------------
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/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-3.18-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/4.3-x86_64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.2)
	/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/4.3-x86_64/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/4.3-x86_64/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/4.3-x86_64/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/4.3-x86_64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.2)
	/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)