Multiple platform build/check report for BioC 3.9 - CHECK report for msa on celaya2

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL msa
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘msa’ ...
** using staged installation
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -I"./gc-7.2/include" -I"./Muscle/" -I"./ClustalW/src" -I"./ClustalOmega/src" -fPIC  -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/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here
#define assert(e)       ((void)0)
        ^
In file included from R_init_msa.cpp:3:
In file included from ./Muscle/RMuscle.h:4:
In file included from ./Muscle/muscle.h:38:
./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
2 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -I"./gc-7.2/include" -I"./Muscle/" -I"./ClustalW/src" -I"./ClustalOmega/src" -fPIC  -Wall -g -O2  -c SplitCharVector2List.cpp -o SplitCharVector2List.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -I"./gc-7.2/include" -I"./Muscle/" -I"./ClustalW/src" -I"./ClustalOmega/src" -fPIC  -Wall -g -O2  -c SplitCharVector2Matrix.cpp -o SplitCharVector2Matrix.o
make --file=msaMakefile --directory=gc-7.2
./configure --enable-cplusplus --enable-threads=pthreads --enable-shared --with-pic
checking build system type... x86_64-apple-darwin15.6.0
checking host system type... x86_64-apple-darwin15.6.0
checking target system type... x86_64-apple-darwin15.6.0
checking GC version numbers... major=7 minor=2 
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... ./install-sh -c -d
checking for gawk... no
checking for mawk... no
checking for nawk... no
checking for awk... awk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking whether to enable maintainer-specific portions of Makefiles... no
checking for style of include used by make... GNU
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc understands -c and -o together... yes
checking dependency style of gcc... gcc3
checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking dependency style of g++... gcc3
checking dependency style of gcc... gcc3
checking for inline... inline
checking for pthread_self in -lpthread... yes
configure: WARNING: "Explicit GC_INIT() calls may be required."
checking for xlc... no
checking whether gcc supports -fno-strict-aliasing... yes
checking whether to build shared libraries... yes
checking which machine-dependent code should be used... 
checking how to print strings... printf
checking for a sed that does not truncate output... /usr/bin/sed
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for fgrep... /usr/bin/grep -F
checking for ld used by gcc... /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... 196608
checking how to convert x86_64-apple-darwin15.6.0 file names to x86_64-apple-darwin15.6.0 format... func_convert_file_noop
checking how to convert x86_64-apple-darwin15.6.0 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... no
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for ar... ar
checking for archiver @FILE support... no
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for sysroot... no
checking for mt... no
checking if : is a manifest tool... no
checking for dsymutil... dsymutil
checking for nmedit... nmedit
checking for lipo... lipo
checking for otool... otool
checking for otool64... no
checking for -single_module linker flag... yes
checking for -exported_symbols_list linker flag... yes
checking for -force_load linker flag... yes
checking how to run the C preprocessor... gcc -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for dlfcn.h... yes
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... yes
checking for gcc option to produce PIC... -fno-common -DPIC
checking if gcc PIC flag -fno-common -DPIC works... yes
checking if gcc static flag -static works... no
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... darwin15.6.0 dyld
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
checking 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... darwin15.6.0 dyld
checking how to hardcode library paths into programs... immediate
checking whether Solaris gcc optimization fix is necessary... no
checking sys/dg_sys_info.h usability... no
checking sys/dg_sys_info.h presence... no
checking for sys/dg_sys_info.h... no
checking for pkg-config... /usr/local/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for ATOMIC_OPS... no
checking which libatomic_ops to use... internal
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating bdw-gc.pc
config.status: creating include/private/config.h
config.status: executing depfiles commands
config.status: executing libtool commands
config.status: executing default commands
=== configuring in libatomic_ops (/Users/biocbuild/bbs-3.9-bioc/meat/msa/src/gc-7.2/libatomic_ops)
configure: running /bin/sh ./configure --disable-option-checking '--prefix=/usr/local'  '--enable-cplusplus' '--enable-threads=pthreads' '--enable-shared' '--with-pic' 'PKG_CONFIG_PATH=/usr/local/opt/libxml2/lib/pkgconfig:/Library/Frameworks/GTK+.framework/Resources/lib/pkgconfig:/usr/lib/pkgconfig:/usr/local/lib/pkgconfig:/usr/X11/lib/pkgconfig:/usr/local/mysql/lib/pkgconfig' --cache-file=/dev/null --srcdir=.
checking build system type... x86_64-apple-darwin15.6.0
checking host system type... x86_64-apple-darwin15.6.0
checking target system type... x86_64-apple-darwin15.6.0
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 supports nested variables... yes
checking for ranlib... ranlib
checking for style of include used by make... GNU
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc understands -c and -o together... yes
checking dependency style of gcc... gcc3
checking dependency style of gcc... gcc3
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for stdlib.h... (cached) yes
checking for unistd.h... (cached) yes
checking for sys/param.h... yes
checking for getpagesize... yes
checking for working mmap... yes
checking for ANSI C header files... (cached) yes
checking for PIC compiler flag... -fPIC
checking whether gcc -fPIC causes __PIC__ definition... yes
checking for pthread_self in -lpthread... yes
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating pkgconfig/atomic_ops.pc
config.status: creating pkgconfig/atomic_ops-uninstalled.pc
config.status: creating doc/Makefile
config.status: creating src/Makefile
config.status: creating src/atomic_ops/Makefile
config.status: creating src/atomic_ops/sysdeps/Makefile
config.status: creating tests/Makefile
config.status: creating src/config.h
config.status: executing depfiles commands
config.status: executing default commands
make
depbase=`echo allchblk.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
	/bin/sh ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src  -fexceptions -g -O2 -fno-strict-aliasing -MT allchblk.lo -MD -MP -MF $depbase.Tpo -c -o allchblk.lo allchblk.c &&\
	mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT allchblk.lo -MD -MP -MF .deps/allchblk.Tpo -c allchblk.c  -fno-common -DPIC -o .libs/allchblk.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT allchblk.lo -MD -MP -MF .deps/allchblk.Tpo -c allchblk.c  -fno-common -DPIC -o allchblk.o >/dev/null 2>&1
depbase=`echo alloc.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
	/bin/sh ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src  -fexceptions -g -O2 -fno-strict-aliasing -MT alloc.lo -MD -MP -MF $depbase.Tpo -c -o alloc.lo alloc.c &&\
	mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT alloc.lo -MD -MP -MF .deps/alloc.Tpo -c alloc.c  -fno-common -DPIC -o .libs/alloc.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT alloc.lo -MD -MP -MF .deps/alloc.Tpo -c alloc.c  -fno-common -DPIC -o alloc.o >/dev/null 2>&1
depbase=`echo blacklst.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
	/bin/sh ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src  -fexceptions -g -O2 -fno-strict-aliasing -MT blacklst.lo -MD -MP -MF $depbase.Tpo -c -o blacklst.lo blacklst.c &&\
	mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT blacklst.lo -MD -MP -MF .deps/blacklst.Tpo -c blacklst.c  -fno-common -DPIC -o .libs/blacklst.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT blacklst.lo -MD -MP -MF .deps/blacklst.Tpo -c blacklst.c  -fno-common -DPIC -o blacklst.o >/dev/null 2>&1
depbase=`echo checksums.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
	/bin/sh ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src  -fexceptions -g -O2 -fno-strict-aliasing -MT checksums.lo -MD -MP -MF $depbase.Tpo -c -o checksums.lo checksums.c &&\
	mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT checksums.lo -MD -MP -MF .deps/checksums.Tpo -c checksums.c  -fno-common -DPIC -o .libs/checksums.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT checksums.lo -MD -MP -MF .deps/checksums.Tpo -c checksums.c  -fno-common -DPIC -o checksums.o >/dev/null 2>&1
depbase=`echo dbg_mlc.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
	/bin/sh ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src  -fexceptions -g -O2 -fno-strict-aliasing -MT dbg_mlc.lo -MD -MP -MF $depbase.Tpo -c -o dbg_mlc.lo dbg_mlc.c &&\
	mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT dbg_mlc.lo -MD -MP -MF .deps/dbg_mlc.Tpo -c dbg_mlc.c  -fno-common -DPIC -o .libs/dbg_mlc.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT dbg_mlc.lo -MD -MP -MF .deps/dbg_mlc.Tpo -c dbg_mlc.c  -fno-common -DPIC -o dbg_mlc.o >/dev/null 2>&1
depbase=`echo dyn_load.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
	/bin/sh ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src  -fexceptions -g -O2 -fno-strict-aliasing -MT dyn_load.lo -MD -MP -MF $depbase.Tpo -c -o dyn_load.lo dyn_load.c &&\
	mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT dyn_load.lo -MD -MP -MF .deps/dyn_load.Tpo -c dyn_load.c  -fno-common -DPIC -o .libs/dyn_load.o
dyn_load.c:1389:37: warning: incompatible pointer types passing 'void (const struct mach_header_64 *, intptr_t)' (aka 'void (const struct mach_header_64 *, long)') to parameter of type 'void (*)(const struct mach_header *, intptr_t)' (aka 'void (*)(const struct mach_header *, long)') [-Wincompatible-pointer-types]
  _dyld_register_func_for_add_image(GC_dyld_image_add);
                                    ^~~~~~~~~~~~~~~~~
/usr/include/mach-o/dyld.h:61:54: note: passing argument to parameter 'func' here
extern void _dyld_register_func_for_add_image(void (*func)(const struct mach_header* mh, intptr_t vmaddr_slide))    __OSX_AVAILABLE_STARTING(__MAC_10_1, __IPHONE_2_0);
                                                     ^
dyn_load.c:1390:40: warning: incompatible pointer types passing 'void (const struct mach_header_64 *, intptr_t)' (aka 'void (const struct mach_header_64 *, long)') to parameter of type 'void (*)(const struct mach_header *, intptr_t)' (aka 'void (*)(const struct mach_header *, long)') [-Wincompatible-pointer-types]
  _dyld_register_func_for_remove_image(GC_dyld_image_remove);
                                       ^~~~~~~~~~~~~~~~~~~~
/usr/include/mach-o/dyld.h:62:57: note: passing argument to parameter 'func' here
extern void _dyld_register_func_for_remove_image(void (*func)(const struct mach_header* mh, intptr_t vmaddr_slide)) __OSX_AVAILABLE_STARTING(__MAC_10_1, __IPHONE_2_0);
                                                        ^
dyn_load.c:1413:12: warning: '_dyld_bind_fully_image_containing_address' is deprecated: first deprecated in macOS 10.5 [-Wdeprecated-declarations]
      if (!_dyld_bind_fully_image_containing_address(
           ^
/usr/include/mach-o/dyld.h:234:13: note: '_dyld_bind_fully_image_containing_address' has been explicitly marked deprecated here
extern bool _dyld_bind_fully_image_containing_address(const void* address)                   __OSX_AVAILABLE_BUT_DEPRECATED(__MAC_10_1,__MAC_10_5,__IPHONE_NA,__IPHONE_NA);
            ^
3 warnings generated.
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT dyn_load.lo -MD -MP -MF .deps/dyn_load.Tpo -c dyn_load.c  -fno-common -DPIC -o dyn_load.o >/dev/null 2>&1
depbase=`echo finalize.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
	/bin/sh ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src  -fexceptions -g -O2 -fno-strict-aliasing -MT finalize.lo -MD -MP -MF $depbase.Tpo -c -o finalize.lo finalize.c &&\
	mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT finalize.lo -MD -MP -MF .deps/finalize.Tpo -c finalize.c  -fno-common -DPIC -o .libs/finalize.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT finalize.lo -MD -MP -MF .deps/finalize.Tpo -c finalize.c  -fno-common -DPIC -o finalize.o >/dev/null 2>&1
depbase=`echo gc_dlopen.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
	/bin/sh ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src  -fexceptions -g -O2 -fno-strict-aliasing -MT gc_dlopen.lo -MD -MP -MF $depbase.Tpo -c -o gc_dlopen.lo gc_dlopen.c &&\
	mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT gc_dlopen.lo -MD -MP -MF .deps/gc_dlopen.Tpo -c gc_dlopen.c  -fno-common -DPIC -o .libs/gc_dlopen.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT gc_dlopen.lo -MD -MP -MF .deps/gc_dlopen.Tpo -c gc_dlopen.c  -fno-common -DPIC -o gc_dlopen.o >/dev/null 2>&1
depbase=`echo gcj_mlc.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
	/bin/sh ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src  -fexceptions -g -O2 -fno-strict-aliasing -MT gcj_mlc.lo -MD -MP -MF $depbase.Tpo -c -o gcj_mlc.lo gcj_mlc.c &&\
	mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT gcj_mlc.lo -MD -MP -MF .deps/gcj_mlc.Tpo -c gcj_mlc.c  -fno-common -DPIC -o .libs/gcj_mlc.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT gcj_mlc.lo -MD -MP -MF .deps/gcj_mlc.Tpo -c gcj_mlc.c  -fno-common -DPIC -o gcj_mlc.o >/dev/null 2>&1
depbase=`echo headers.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
	/bin/sh ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src  -fexceptions -g -O2 -fno-strict-aliasing -MT headers.lo -MD -MP -MF $depbase.Tpo -c -o headers.lo headers.c &&\
	mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT headers.lo -MD -MP -MF .deps/headers.Tpo -c headers.c  -fno-common -DPIC -o .libs/headers.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT headers.lo -MD -MP -MF .deps/headers.Tpo -c headers.c  -fno-common -DPIC -o headers.o >/dev/null 2>&1
depbase=`echo malloc.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
	/bin/sh ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src  -fexceptions -g -O2 -fno-strict-aliasing -MT malloc.lo -MD -MP -MF $depbase.Tpo -c -o malloc.lo malloc.c &&\
	mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT malloc.lo -MD -MP -MF .deps/malloc.Tpo -c malloc.c  -fno-common -DPIC -o .libs/malloc.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT malloc.lo -MD -MP -MF .deps/malloc.Tpo -c malloc.c  -fno-common -DPIC -o malloc.o >/dev/null 2>&1
depbase=`echo mallocx.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
	/bin/sh ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src  -fexceptions -g -O2 -fno-strict-aliasing -MT mallocx.lo -MD -MP -MF $depbase.Tpo -c -o mallocx.lo mallocx.c &&\
	mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT mallocx.lo -MD -MP -MF .deps/mallocx.Tpo -c mallocx.c  -fno-common -DPIC -o .libs/mallocx.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT mallocx.lo -MD -MP -MF .deps/mallocx.Tpo -c mallocx.c  -fno-common -DPIC -o mallocx.o >/dev/null 2>&1
depbase=`echo mark.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
	/bin/sh ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src  -fexceptions -g -O2 -fno-strict-aliasing -MT mark.lo -MD -MP -MF $depbase.Tpo -c -o mark.lo mark.c &&\
	mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT mark.lo -MD -MP -MF .deps/mark.Tpo -c mark.c  -fno-common -DPIC -o .libs/mark.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT mark.lo -MD -MP -MF .deps/mark.Tpo -c mark.c  -fno-common -DPIC -o mark.o >/dev/null 2>&1
depbase=`echo mark_rts.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
	/bin/sh ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src  -fexceptions -g -O2 -fno-strict-aliasing -MT mark_rts.lo -MD -MP -MF $depbase.Tpo -c -o mark_rts.lo mark_rts.c &&\
	mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT mark_rts.lo -MD -MP -MF .deps/mark_rts.Tpo -c mark_rts.c  -fno-common -DPIC -o .libs/mark_rts.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT mark_rts.lo -MD -MP -MF .deps/mark_rts.Tpo -c mark_rts.c  -fno-common -DPIC -o mark_rts.o >/dev/null 2>&1
depbase=`echo misc.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
	/bin/sh ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src  -fexceptions -g -O2 -fno-strict-aliasing -MT misc.lo -MD -MP -MF $depbase.Tpo -c -o misc.lo misc.c &&\
	mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT misc.lo -MD -MP -MF .deps/misc.Tpo -c misc.c  -fno-common -DPIC -o .libs/misc.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT misc.lo -MD -MP -MF .deps/misc.Tpo -c misc.c  -fno-common -DPIC -o misc.o >/dev/null 2>&1
depbase=`echo new_hblk.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
	/bin/sh ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src  -fexceptions -g -O2 -fno-strict-aliasing -MT new_hblk.lo -MD -MP -MF $depbase.Tpo -c -o new_hblk.lo new_hblk.c &&\
	mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT new_hblk.lo -MD -MP -MF .deps/new_hblk.Tpo -c new_hblk.c  -fno-common -DPIC -o .libs/new_hblk.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT new_hblk.lo -MD -MP -MF .deps/new_hblk.Tpo -c new_hblk.c  -fno-common -DPIC -o new_hblk.o >/dev/null 2>&1
depbase=`echo obj_map.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
	/bin/sh ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src  -fexceptions -g -O2 -fno-strict-aliasing -MT obj_map.lo -MD -MP -MF $depbase.Tpo -c -o obj_map.lo obj_map.c &&\
	mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT obj_map.lo -MD -MP -MF .deps/obj_map.Tpo -c obj_map.c  -fno-common -DPIC -o .libs/obj_map.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT obj_map.lo -MD -MP -MF .deps/obj_map.Tpo -c obj_map.c  -fno-common -DPIC -o obj_map.o >/dev/null 2>&1
depbase=`echo os_dep.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
	/bin/sh ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src  -fexceptions -g -O2 -fno-strict-aliasing -MT os_dep.lo -MD -MP -MF $depbase.Tpo -c -o os_dep.lo os_dep.c &&\
	mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT os_dep.lo -MD -MP -MF .deps/os_dep.Tpo -c os_dep.c  -fno-common -DPIC -o .libs/os_dep.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT os_dep.lo -MD -MP -MF .deps/os_dep.Tpo -c os_dep.c  -fno-common -DPIC -o os_dep.o >/dev/null 2>&1
depbase=`echo pcr_interface.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
	/bin/sh ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src  -fexceptions -g -O2 -fno-strict-aliasing -MT pcr_interface.lo -MD -MP -MF $depbase.Tpo -c -o pcr_interface.lo pcr_interface.c &&\
	mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT pcr_interface.lo -MD -MP -MF .deps/pcr_interface.Tpo -c pcr_interface.c  -fno-common -DPIC -o .libs/pcr_interface.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT pcr_interface.lo -MD -MP -MF .deps/pcr_interface.Tpo -c pcr_interface.c  -fno-common -DPIC -o pcr_interface.o >/dev/null 2>&1
depbase=`echo ptr_chck.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
	/bin/sh ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src  -fexceptions -g -O2 -fno-strict-aliasing -MT ptr_chck.lo -MD -MP -MF $depbase.Tpo -c -o ptr_chck.lo ptr_chck.c &&\
	mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT ptr_chck.lo -MD -MP -MF .deps/ptr_chck.Tpo -c ptr_chck.c  -fno-common -DPIC -o .libs/ptr_chck.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT ptr_chck.lo -MD -MP -MF .deps/ptr_chck.Tpo -c ptr_chck.c  -fno-common -DPIC -o ptr_chck.o >/dev/null 2>&1
depbase=`echo real_malloc.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
	/bin/sh ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src  -fexceptions -g -O2 -fno-strict-aliasing -MT real_malloc.lo -MD -MP -MF $depbase.Tpo -c -o real_malloc.lo real_malloc.c &&\
	mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT real_malloc.lo -MD -MP -MF .deps/real_malloc.Tpo -c real_malloc.c  -fno-common -DPIC -o .libs/real_malloc.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT real_malloc.lo -MD -MP -MF .deps/real_malloc.Tpo -c real_malloc.c  -fno-common -DPIC -o real_malloc.o >/dev/null 2>&1
depbase=`echo reclaim.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
	/bin/sh ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src  -fexceptions -g -O2 -fno-strict-aliasing -MT reclaim.lo -MD -MP -MF $depbase.Tpo -c -o reclaim.lo reclaim.c &&\
	mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT reclaim.lo -MD -MP -MF .deps/reclaim.Tpo -c reclaim.c  -fno-common -DPIC -o .libs/reclaim.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT reclaim.lo -MD -MP -MF .deps/reclaim.Tpo -c reclaim.c  -fno-common -DPIC -o reclaim.o >/dev/null 2>&1
depbase=`echo specific.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
	/bin/sh ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src  -fexceptions -g -O2 -fno-strict-aliasing -MT specific.lo -MD -MP -MF $depbase.Tpo -c -o specific.lo specific.c &&\
	mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT specific.lo -MD -MP -MF .deps/specific.Tpo -c specific.c  -fno-common -DPIC -o .libs/specific.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT specific.lo -MD -MP -MF .deps/specific.Tpo -c specific.c  -fno-common -DPIC -o specific.o >/dev/null 2>&1
depbase=`echo stubborn.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
	/bin/sh ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src  -fexceptions -g -O2 -fno-strict-aliasing -MT stubborn.lo -MD -MP -MF $depbase.Tpo -c -o stubborn.lo stubborn.c &&\
	mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT stubborn.lo -MD -MP -MF .deps/stubborn.Tpo -c stubborn.c  -fno-common -DPIC -o .libs/stubborn.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT stubborn.lo -MD -MP -MF .deps/stubborn.Tpo -c stubborn.c  -fno-common -DPIC -o stubborn.o >/dev/null 2>&1
depbase=`echo typd_mlc.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
	/bin/sh ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src  -fexceptions -g -O2 -fno-strict-aliasing -MT typd_mlc.lo -MD -MP -MF $depbase.Tpo -c -o typd_mlc.lo typd_mlc.c &&\
	mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT typd_mlc.lo -MD -MP -MF .deps/typd_mlc.Tpo -c typd_mlc.c  -fno-common -DPIC -o .libs/typd_mlc.o
typd_mlc.c:363:37: warning: shifting a negative signed value is undefined [-Wshift-negative-value]
                            (((word)WORDS_TO_BYTES(-1)) | GC_DS_PER_OBJECT),
                                    ^~~~~~~~~~~~~~~~~~
./include/private/gc_priv.h:565:35: note: expanded from macro 'WORDS_TO_BYTES'
#  define WORDS_TO_BYTES(x)   ((x)<<3)
                               ~~~^
1 warning generated.
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT typd_mlc.lo -MD -MP -MF .deps/typd_mlc.Tpo -c typd_mlc.c  -fno-common -DPIC -o typd_mlc.o >/dev/null 2>&1
depbase=`echo backgraph.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
	/bin/sh ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src  -fexceptions -g -O2 -fno-strict-aliasing -MT backgraph.lo -MD -MP -MF $depbase.Tpo -c -o backgraph.lo backgraph.c &&\
	mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT backgraph.lo -MD -MP -MF .deps/backgraph.Tpo -c backgraph.c  -fno-common -DPIC -o .libs/backgraph.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT backgraph.lo -MD -MP -MF .deps/backgraph.Tpo -c backgraph.c  -fno-common -DPIC -o backgraph.o >/dev/null 2>&1
depbase=`echo thread_local_alloc.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
	/bin/sh ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src  -fexceptions -g -O2 -fno-strict-aliasing -MT thread_local_alloc.lo -MD -MP -MF $depbase.Tpo -c -o thread_local_alloc.lo thread_local_alloc.c &&\
	mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT thread_local_alloc.lo -MD -MP -MF .deps/thread_local_alloc.Tpo -c thread_local_alloc.c  -fno-common -DPIC -o .libs/thread_local_alloc.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT thread_local_alloc.lo -MD -MP -MF .deps/thread_local_alloc.Tpo -c thread_local_alloc.c  -fno-common -DPIC -o thread_local_alloc.o >/dev/null 2>&1
depbase=`echo pthread_start.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
	/bin/sh ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src  -fexceptions -g -O2 -fno-strict-aliasing -MT pthread_start.lo -MD -MP -MF $depbase.Tpo -c -o pthread_start.lo pthread_start.c &&\
	mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT pthread_start.lo -MD -MP -MF .deps/pthread_start.Tpo -c pthread_start.c  -fno-common -DPIC -o .libs/pthread_start.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT pthread_start.lo -MD -MP -MF .deps/pthread_start.Tpo -c pthread_start.c  -fno-common -DPIC -o pthread_start.o >/dev/null 2>&1
depbase=`echo pthread_support.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
	/bin/sh ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src  -fexceptions -g -O2 -fno-strict-aliasing -MT pthread_support.lo -MD -MP -MF $depbase.Tpo -c -o pthread_support.lo pthread_support.c &&\
	mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT pthread_support.lo -MD -MP -MF .deps/pthread_support.Tpo -c pthread_support.c  -fno-common -DPIC -o .libs/pthread_support.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT pthread_support.lo -MD -MP -MF .deps/pthread_support.Tpo -c pthread_support.c  -fno-common -DPIC -o pthread_support.o >/dev/null 2>&1
depbase=`echo pthread_stop_world.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
	/bin/sh ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src  -fexceptions -g -O2 -fno-strict-aliasing -MT pthread_stop_world.lo -MD -MP -MF $depbase.Tpo -c -o pthread_stop_world.lo pthread_stop_world.c &&\
	mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT pthread_stop_world.lo -MD -MP -MF .deps/pthread_stop_world.Tpo -c pthread_stop_world.c  -fno-common -DPIC -o .libs/pthread_stop_world.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT pthread_stop_world.lo -MD -MP -MF .deps/pthread_stop_world.Tpo -c pthread_stop_world.c  -fno-common -DPIC -o pthread_stop_world.o >/dev/null 2>&1
depbase=`echo darwin_stop_world.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
	/bin/sh ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src  -fexceptions -g -O2 -fno-strict-aliasing -MT darwin_stop_world.lo -MD -MP -MF $depbase.Tpo -c -o darwin_stop_world.lo darwin_stop_world.c &&\
	mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT darwin_stop_world.lo -MD -MP -MF .deps/darwin_stop_world.Tpo -c darwin_stop_world.c  -fno-common -DPIC -o .libs/darwin_stop_world.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT darwin_stop_world.lo -MD -MP -MF .deps/darwin_stop_world.Tpo -c darwin_stop_world.c  -fno-common -DPIC -o darwin_stop_world.o >/dev/null 2>&1
depbase=`echo libatomic_ops/src/atomic_ops.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
	/bin/sh ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src  -fexceptions -g -O2 -fno-strict-aliasing -MT libatomic_ops/src/atomic_ops.lo -MD -MP -MF $depbase.Tpo -c -o libatomic_ops/src/atomic_ops.lo libatomic_ops/src/atomic_ops.c &&\
	mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT libatomic_ops/src/atomic_ops.lo -MD -MP -MF libatomic_ops/src/.deps/atomic_ops.Tpo -c libatomic_ops/src/atomic_ops.c  -fno-common -DPIC -o libatomic_ops/src/.libs/atomic_ops.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT libatomic_ops/src/atomic_ops.lo -MD -MP -MF libatomic_ops/src/.deps/atomic_ops.Tpo -c libatomic_ops/src/atomic_ops.c  -fno-common -DPIC -o libatomic_ops/src/atomic_ops.o >/dev/null 2>&1
depbase=`echo mach_dep.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
	/bin/sh ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src  -fexceptions -g -O2 -fno-strict-aliasing -MT mach_dep.lo -MD -MP -MF $depbase.Tpo -c -o mach_dep.lo mach_dep.c &&\
	mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT mach_dep.lo -MD -MP -MF .deps/mach_dep.Tpo -c mach_dep.c  -fno-common -DPIC -o .libs/mach_dep.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT mach_dep.lo -MD -MP -MF .deps/mach_dep.Tpo -c mach_dep.c  -fno-common -DPIC -o mach_dep.o >/dev/null 2>&1
/bin/sh ./libtool  --tag=CC   --mode=link gcc -fexceptions -g -O2 -fno-strict-aliasing -Wl,-single_module -version-info 1:3:0 -no-undefined  -o libgc.la -rpath /usr/local/lib allchblk.lo alloc.lo blacklst.lo checksums.lo dbg_mlc.lo dyn_load.lo finalize.lo gc_dlopen.lo gcj_mlc.lo headers.lo malloc.lo mallocx.lo mark.lo mark_rts.lo misc.lo new_hblk.lo obj_map.lo os_dep.lo pcr_interface.lo ptr_chck.lo real_malloc.lo reclaim.lo specific.lo stubborn.lo typd_mlc.lo backgraph.lo thread_local_alloc.lo pthread_start.lo pthread_support.lo pthread_stop_world.lo darwin_stop_world.lo  libatomic_ops/src/atomic_ops.lo mach_dep.lo -lpthread   
libtool: link: gcc -dynamiclib  -o .libs/libgc.1.dylib  .libs/allchblk.o .libs/alloc.o .libs/blacklst.o .libs/checksums.o .libs/dbg_mlc.o .libs/dyn_load.o .libs/finalize.o .libs/gc_dlopen.o .libs/gcj_mlc.o .libs/headers.o .libs/malloc.o .libs/mallocx.o .libs/mark.o .libs/mark_rts.o .libs/misc.o .libs/new_hblk.o .libs/obj_map.o .libs/os_dep.o .libs/pcr_interface.o .libs/ptr_chck.o .libs/real_malloc.o .libs/reclaim.o .libs/specific.o .libs/stubborn.o .libs/typd_mlc.o .libs/backgraph.o .libs/thread_local_alloc.o .libs/pthread_start.o .libs/pthread_support.o .libs/pthread_stop_world.o .libs/darwin_stop_world.o libatomic_ops/src/.libs/atomic_ops.o .libs/mach_dep.o   -lpthread  -g -O2 -Wl,-single_module   -install_name  /usr/local/lib/libgc.1.dylib -compatibility_version 2 -current_version 2.3 -Wl,-single_module
libtool: link: (cd ".libs" && rm -f "libgc.dylib" && ln -s "libgc.1.dylib" "libgc.dylib")
libtool: link: ar cru .libs/libgc.a  allchblk.o alloc.o blacklst.o checksums.o dbg_mlc.o dyn_load.o finalize.o gc_dlopen.o gcj_mlc.o headers.o malloc.o mallocx.o mark.o mark_rts.o misc.o new_hblk.o obj_map.o os_dep.o pcr_interface.o ptr_chck.o real_malloc.o reclaim.o specific.o stubborn.o typd_mlc.o backgraph.o thread_local_alloc.o pthread_start.o pthread_support.o pthread_stop_world.o darwin_stop_world.o libatomic_ops/src/atomic_ops.o mach_dep.o
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libgc.a(checksums.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libgc.a(gc_dlopen.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libgc.a(pcr_interface.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libgc.a(real_malloc.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libgc.a(specific.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libgc.a(backgraph.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libgc.a(pthread_stop_world.o) has no symbols
libtool: link: ranlib .libs/libgc.a
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libgc.a(checksums.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libgc.a(gc_dlopen.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libgc.a(pcr_interface.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libgc.a(real_malloc.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libgc.a(specific.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libgc.a(backgraph.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: .libs/libgc.a(pthread_stop_world.o) has no symbols
libtool: link: ( cd ".libs" && rm -f "libgc.la" && ln -s "../libgc.la" "libgc.la" )
depbase=`echo gc_cpp.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
	/bin/sh ./libtool  --tag=CXX   --mode=compile g++ -DHAVE_CONFIG_H   -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src  -fexceptions -g -O2 -MT gc_cpp.lo -MD -MP -MF $depbase.Tpo -c -o gc_cpp.lo gc_cpp.cc &&\
	mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  g++ -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -MT gc_cpp.lo -MD -MP -MF .deps/gc_cpp.Tpo -c gc_cpp.cc  -fno-common -DPIC -o .libs/gc_cpp.o
gc_cpp.cc:37:7: warning: 'operator new' is missing exception specification 'throw(std::bad_alloc)' [-Wmissing-exception-spec]
void* operator new( size_t size ) {
      ^
                                  throw(std::bad_alloc)
gc_cpp.cc:41:8: warning: 'operator delete' is missing exception specification 'throw()' [-Wmissing-exception-spec]
  void operator delete( void* obj ) {
       ^
                                    throw()
gc_cpp.cc:48:7: warning: 'operator new[]' is missing exception specification 'throw(std::bad_alloc)' [-Wmissing-exception-spec]
void* operator new[]( size_t size ) {
      ^
                                    throw(std::bad_alloc)
gc_cpp.cc:51:6: warning: 'operator delete[]' is missing exception specification 'throw()' [-Wmissing-exception-spec]
void operator delete[]( void* obj ) {
     ^
                                    throw()
4 warnings generated.
libtool: compile:  g++ -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -MT gc_cpp.lo -MD -MP -MF .deps/gc_cpp.Tpo -c gc_cpp.cc  -fno-common -DPIC -o gc_cpp.o >/dev/null 2>&1
/bin/sh ./libtool  --tag=CXX   --mode=link g++ -fexceptions -g -O2 -version-info 1:3:0 -no-undefined  -o libgccpp.la -rpath /usr/local/lib gc_cpp.lo ./libgc.la 
libtool: link: g++ -dynamiclib  -o .libs/libgccpp.1.dylib  .libs/gc_cpp.o   ./.libs/libgc.dylib -lpthread  -g -O2   -install_name  /usr/local/lib/libgccpp.1.dylib -compatibility_version 2 -current_version 2.3 -Wl,-single_module
libtool: link: (cd ".libs" && rm -f "libgccpp.dylib" && ln -s "libgccpp.1.dylib" "libgccpp.dylib")
libtool: link: ar cru .libs/libgccpp.a  gc_cpp.o
libtool: link: ranlib .libs/libgccpp.a
libtool: link: ( cd ".libs" && rm -f "libgccpp.la" && ln -s "../libgccpp.la" "libgccpp.la" )
depbase=`echo cord/cordbscs.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
	/bin/sh ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src  -fexceptions -g -O2 -fno-strict-aliasing -MT cord/cordbscs.lo -MD -MP -MF $depbase.Tpo -c -o cord/cordbscs.lo cord/cordbscs.c &&\
	mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT cord/cordbscs.lo -MD -MP -MF cord/.deps/cordbscs.Tpo -c cord/cordbscs.c  -fno-common -DPIC -o cord/.libs/cordbscs.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT cord/cordbscs.lo -MD -MP -MF cord/.deps/cordbscs.Tpo -c cord/cordbscs.c  -fno-common -DPIC -o cord/cordbscs.o >/dev/null 2>&1
depbase=`echo cord/cordprnt.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
	/bin/sh ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src  -fexceptions -g -O2 -fno-strict-aliasing -MT cord/cordprnt.lo -MD -MP -MF $depbase.Tpo -c -o cord/cordprnt.lo cord/cordprnt.c &&\
	mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT cord/cordprnt.lo -MD -MP -MF cord/.deps/cordprnt.Tpo -c cord/cordprnt.c  -fno-common -DPIC -o cord/.libs/cordprnt.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT cord/cordprnt.lo -MD -MP -MF cord/.deps/cordprnt.Tpo -c cord/cordprnt.c  -fno-common -DPIC -o cord/cordprnt.o >/dev/null 2>&1
depbase=`echo cord/cordtest.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
	/bin/sh ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src  -fexceptions -g -O2 -fno-strict-aliasing -MT cord/cordtest.lo -MD -MP -MF $depbase.Tpo -c -o cord/cordtest.lo cord/cordtest.c &&\
	mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT cord/cordtest.lo -MD -MP -MF cord/.deps/cordtest.Tpo -c cord/cordtest.c  -fno-common -DPIC -o cord/.libs/cordtest.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT cord/cordtest.lo -MD -MP -MF cord/.deps/cordtest.Tpo -c cord/cordtest.c  -fno-common -DPIC -o cord/cordtest.o >/dev/null 2>&1
depbase=`echo cord/cordxtra.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
	/bin/sh ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H   -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src  -fexceptions -g -O2 -fno-strict-aliasing -MT cord/cordxtra.lo -MD -MP -MF $depbase.Tpo -c -o cord/cordxtra.lo cord/cordxtra.c &&\
	mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT cord/cordxtra.lo -MD -MP -MF cord/.deps/cordxtra.Tpo -c cord/cordxtra.c  -fno-common -DPIC -o cord/.libs/cordxtra.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT cord/cordxtra.lo -MD -MP -MF cord/.deps/cordxtra.Tpo -c cord/cordxtra.c  -fno-common -DPIC -o cord/cordxtra.o >/dev/null 2>&1
/bin/sh ./libtool  --tag=CC   --mode=link gcc -fexceptions -g -O2 -fno-strict-aliasing -version-info 1:3:0 -no-undefined  -o libcord.la -rpath /usr/local/lib cord/cordbscs.lo cord/cordprnt.lo cord/cordtest.lo cord/cordxtra.lo ./libgc.la 
libtool: link: gcc -dynamiclib  -o .libs/libcord.1.dylib  cord/.libs/cordbscs.o cord/.libs/cordprnt.o cord/.libs/cordtest.o cord/.libs/cordxtra.o   ./.libs/libgc.dylib -lpthread  -g -O2   -install_name  /usr/local/lib/libcord.1.dylib -compatibility_version 2 -current_version 2.3 -Wl,-single_module
libtool: link: (cd ".libs" && rm -f "libcord.dylib" && ln -s "libcord.1.dylib" "libcord.dylib")
libtool: link: ar cru .libs/libcord.a  cord/cordbscs.o cord/cordprnt.o cord/cordtest.o cord/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-7.2/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
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c aligngivenpath.cpp -o aligngivenpath.o
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)
              ^
7 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c aligngivenpathsw.cpp -o aligngivenpathsw.o
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)
              ^
7 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c aligntwomsas.cpp -o aligntwomsas.o
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)
              ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c aligntwoprofs.cpp -o aligntwoprofs.o
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)
              ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c aln.cpp -o aln.o
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)
              ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c alpha.cpp -o alpha.o
alpha.cpp:84:10: warning: enumeration value 'ALPHA_Undefined' not handled in switch [-Wswitch]
        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)
              ^
2 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c anchors.cpp -o anchors.o
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[],
            ^
4 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c bittraceback.cpp -o bittraceback.o
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)
                   ^
3 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c blosum62.cpp -o blosum62.o
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)
              ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c blosumla.cpp -o blosumla.o
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] =
             ^
2 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c clust.cpp -o clust.o
clust.cpp:167:10: warning: enumeration value 'JOIN_Undefined' not handled in switch [-Wswitch]
        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: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)
                ^
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)
              ^
7 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c cluster.cpp -o cluster.o
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)
                    ^
4 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c clwwt.cpp -o clwwt.o
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)
              ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c color.cpp -o color.o
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)
           ^
25 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c cons.cpp -o cons.o
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)
              ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c diaglist.cpp -o diaglist.o
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)
              ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c diffobjscore.cpp -o diffobjscore.o
diffobjscore.cpp:76:17: warning: unused variable 'uSeqCount' [-Wunused-variable]
        const unsigned uSeqCount = msa.GetSeqCount();
                       ^
diffobjscore.cpp:77:17: warning: unused variable 'uColCount' [-Wunused-variable]
        const unsigned uColCount = msa.GetColCount();
                       ^
In file included from diffobjscore.cpp:1:
In file included from ./muscle.h:38:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
3 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c diffpaths.cpp -o diffpaths.o
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)
              ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c difftrees.cpp -o difftrees.o
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)
              ^
2 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c difftreese.cpp -o difftreese.o
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)
              ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c distcalc.cpp -o distcalc.o
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)
              ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c distfunc.cpp -o distfunc.o
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)
              ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c distpwkimura.cpp -o distpwkimura.o
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)
              ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c domuscle.cpp -o domuscle.o
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)
              ^
2 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c dosp.cpp -o dosp.o
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)
              ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c dpreglist.cpp -o dpreglist.o
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)
              ^
2 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c drawtree.cpp -o drawtree.o
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)
              ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c edgelist.cpp -o edgelist.o
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)
              ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c enumopts.cpp -o enumopts.o
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,
                        ^~~~~~~~~~~
:101:1: 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,
                        ^~~~~~~~~~~
:104:1: 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,
                        ^~~~~~~~~~~
:107:1: 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,
                        ^~~~~~~~~~~
:109:1: 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,
                        ^~~~~~~~~~~
:109:1: 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,
                        ^~~~~~~~~~~
:109:1: 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,
                        ^~~~~~~~~~~
:109:1: 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,
                        ^~~~~~~~~~~
:109:1: 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,
                        ^~~~~~~~~~~
:109:1: 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,
                        ^~~~~~~~~~~
:109:1: 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,
                        ^~~~~~~~~~~
:109:1: 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,
                        ^~~~~~~~~~~
:109:1: 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,
                        ^~~~~~~~~~~
:109:1: 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,
                        ^~~~~~~~~~~
:109:1: 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,
                        ^~~~~~~~~~~
:109:1: 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,
                        ^~~~~~~~~~~
:109:1: 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,
                        ^~~~~~~~~~~
:109:1: 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,
                        ^~~~~~~~~~~
:109:1: 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,
                        ^~~~~~~~~~~
:109:1: 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,
                        ^~~~~~~~~~~
:109:1: 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,
                        ^~~~~~~~~~~
:109:1: 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,
                        ^~~~~~~~~~~
:109:1: 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,
                        ^~~~~~~~~~~
:109:1: 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,
                        ^~~~~~~~~~~
:109:1: 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,
                        ^~~~~~~~~~~
:109:1: 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,
                        ^~~~~~~~~~~
:109:1: 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,
                        ^~~~~~~~~~~
:109:1: 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,
                        ^~~~~~~~~~~
:109:1: 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,
                        ^~~~~~~~~~~
:109:1: 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,
                        ^~~~~~~~~~~
:109:1: 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,
                        ^~~~~~~~~~~
:109:1: 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,
                        ^~~~~~~~~~~
:109:1: 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,
                        ^~~~~~~~~~~
:109:1: 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,
                        ^~~~~~~~~~~
:109:1: 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,
                        ^~~~~~~~~~~
:109:1: 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,
                        ^~~~~~~~~~~
:109:1: 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,
                        ^~~~~~~~~~~
:109:1: 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,
                        ^~~~~~~~~~~
:109:1: 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,
                        ^~~~~~~~~~~
:109:1: 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,
                        ^~~~~~~~~~~
:109:1: 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,
                        ^~~~~~~~~~~
:109:1: 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,
                        ^~~~~~~~~~~
:109:1: 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,
                        ^~~~~~~~~~~
:109:1: 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,
                        ^~~~~~~~~~~
:109:1: 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,
                        ^~~~~~~~~~~
:109:1: 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,
                        ^~~~~~~~~~~
:109:1: 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,
                        ^~~~~~~~~~~
:109:1: 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,
                        ^~~~~~~~~~~
:109:1: 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,
                        ^~~~~~~~~~~
:109:1: 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,
                        ^~~~~~~~~~~
:109:1: 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,
                        ^~~~~~~~~~~
:109:1: 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,
                        ^~~~~~~~~~~
:109:1: 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)
              ^
64 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c enumtostr.cpp -o enumtostr.o
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)
              ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c estring.cpp -o estring.o
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[])
            ^
5 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c fasta.cpp -o fasta.o
fasta.cpp:16:11: warning: unused variable 'uColCount' [-Wunused-variable]
        unsigned uColCount = uInsane;
                 ^
fasta.cpp:15:11: warning: unused variable 'uSeqCount' [-Wunused-variable]
        unsigned uSeqCount = 0;
                 ^
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)
              ^
3 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c fasta2.cpp -o fasta2.o
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)
              ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c fastclust.cpp -o fastclust.o
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)
              ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c fastdist.cpp -o fastdist.o
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)
              ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c fastdistjones.cpp -o fastdistjones.o
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)
              ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c fastdistkbit.cpp -o fastdistkbit.o
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)
              ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c fastdistkmer.cpp -o fastdistkmer.o
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)
              ^
2 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c fastdistmafft.cpp -o fastdistmafft.o
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[])
            ^
3 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c fastdistnuc.cpp -o fastdistnuc.o
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[])
            ^
4 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c fastscorepath2.cpp -o fastscorepath2.o
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)
              ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c finddiags.cpp -o finddiags.o
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)
             ^
2 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c finddiagsn.cpp -o finddiagsn.o
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)
             ^
2 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c glbalign.cpp -o glbalign.o
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)
              ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c glbalign352.cpp -o glbalign352.o
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)
              ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c glbaligndiag.cpp -o glbaligndiag.o
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)
              ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c glbalignle.cpp -o glbalignle.o
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)
              ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c glbalignsimple.cpp -o glbalignsimple.o
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,
            ^
3 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c glbalignsp.cpp -o glbalignsp.o
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)
              ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c glbalignspn.cpp -o glbalignspn.o
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)
              ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c glbalignss.cpp -o glbalignss.o
glbalignss.cpp:177:16: warning: unused variable 'ptrRowA' [-Wunused-variable]
                const SCORE *ptrRowA = MxRowA[i];
                             ^
glbalignss.cpp:120:17: warning: unused variable 'uPrefixCountB' [-Wunused-variable]
        const unsigned uPrefixCountB = uLengthB + 1;
                       ^
glbalignss.cpp:119:17: warning: unused variable 'uPrefixCountA' [-Wunused-variable]
        const unsigned uPrefixCountA = uLengthA + 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)
             ^
5 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c glbalndimer.cpp -o glbalndimer.o
glbalndimer.cpp:123:10: warning: enumeration values 'PPSCORE_Undefined' and 'PPSCORE_SPN' not handled in switch [-Wswitch]
        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)
                   ^
3 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c globals.cpp -o globals.o
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)
              ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c globalslinux.cpp -o globalslinux.o
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)
              ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c globalsosx.cpp -o globalsosx.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c globalsother.cpp -o globalsother.o
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)
              ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c globalswin32.cpp -o globalswin32.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c gonnet.cpp -o gonnet.o
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] =
             ^
2 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c henikoffweight.cpp -o henikoffweight.o
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)
              ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c henikoffweightpb.cpp -o henikoffweightpb.o
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)
              ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c html.cpp -o html.o
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)
              ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c hydro.cpp -o hydro.o
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)
              ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c intmath.cpp -o intmath.o
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)
              ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c local.cpp -o local.o
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)
              ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c main.cpp -o main.o
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)
              ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c makerootmsa.cpp -o makerootmsa.o
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)
            ^
5 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c makerootmsab.cpp -o makerootmsab.o
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)
              ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c maketree.cpp -o maketree.o
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)
              ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c mhack.cpp -o mhack.o
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)
              ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c mpam200.cpp -o mpam200.o
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)
              ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c msa.cpp -o msa.o
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)
            ^
5 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c msa2.cpp -o msa2.o
msa2.cpp:357:10: warning: enumeration value 'SEQWEIGHT_Undefined' not handled in switch [-Wswitch]
        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)
              ^
3 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c msadistkimura.cpp -o msadistkimura.o
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)
              ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c msf.cpp -o msf.o
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)
                   ^
2 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c muscle.cpp -o muscle.o
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)
              ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c muscleout.cpp -o muscleout.o
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)
              ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c nucmx.cpp -o nucmx.o
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)
              ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c nwdasimple.cpp -o nwdasimple.o
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)
              ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c nwdasimple2.cpp -o nwdasimple2.o
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)
              ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c nwdasmall.cpp -o nwdasmall.o
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)
              ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c nwrec.cpp -o nwrec.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c nwsmall.cpp -o nwsmall.o
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)
                   ^
6 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c objscore.cpp -o objscore.o
objscore.cpp:31:10: warning: enumeration values 'OBJSCORE_Undefined' and 'OBJSCORE_SPM' not handled in switch [-Wswitch]
        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)
              ^
2 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c objscore2.cpp -o objscore2.o
objscore2.cpp:22:10: warning: enumeration value 'TERMGAPS_Undefined' not handled in switch [-Wswitch]
        switch (g_TermGaps)
                ^
objscore2.cpp:62:8: warning: unused variable 'scoreGaps' [-Wunused-variable]
        SCORE scoreGaps = 0;
              ^
objscore2.cpp:64:7: warning: unused variable 'bGapping2' [-Wunused-variable]
        bool bGapping2 = false;
             ^
objscore2.cpp:63:7: warning: unused variable 'bGapping1' [-Wunused-variable]
        bool bGapping1 = 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)
              ^
7 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c objscoreda.cpp -o objscoreda.o
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)
              ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c onexception.cpp -o onexception.o
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)
              ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c options.cpp -o options.o
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)
              ^
102 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c outweights.cpp -o outweights.o
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)
              ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c pam200mafft.cpp -o pam200mafft.o
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] =
             ^
25 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c params.cpp -o params.o
params.cpp:441:10: warning: enumeration value 'PPSCORE_Undefined' not handled in switch [-Wswitch]
        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)
              ^
2 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c phy.cpp -o phy.o
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)
              ^
2 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c phy2.cpp -o phy2.o
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)
              ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c phy3.cpp -o phy3.o
phy3.cpp:125:15: warning: unused variable 'dThisDist' [-Wunused-variable]
        const double dThisDist = tree.GetEdgeLength(uNode1, uNode2);
                     ^
phy3.cpp:191:11: warning: unused variable 'uMaxFrom' [-Wunused-variable]
        unsigned uMaxFrom = NULL_NEIGHBOR;
                 ^
phy3.cpp:192:11: warning: unused variable 'uMaxTo' [-Wunused-variable]
        unsigned uMaxTo = NULL_NEIGHBOR;
                 ^
phy3.cpp:167:17: warning: unused variable 'uLeafCount' [-Wunused-variable]
        const unsigned uLeafCount = tree.GetLeafCount();
                       ^
phy3.cpp:190:9: warning: unused variable 'dAllMaxDist' [-Wunused-variable]
        double dAllMaxDist = -1e20;
               ^
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)
            ^
7 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c phy4.cpp -o phy4.o
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)
              ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c phyfromclust.cpp -o phyfromclust.o
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)
              ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c phyfromfile.cpp -o phyfromfile.o
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)
              ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c physeq.cpp -o physeq.o
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)
              ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c phytofile.cpp -o phytofile.o
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)
              ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c posgap.cpp -o posgap.o
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)
              ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c ppscore.cpp -o ppscore.o
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)
              ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c profdb.cpp -o profdb.o
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)
                       ^
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)
              ^
2 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c profile.cpp -o profile.o
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)
              ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c profilefrommsa.cpp -o profilefrommsa.o
profilefrommsa.cpp:230:10: warning: enumeration value 'ALPHA_Undefined' not handled in switch [-Wswitch]
        switch (g_Alpha)
                ^
profilefrommsa.cpp:245:17: warning: unused variable 'uSeqCount' [-Wunused-variable]
        const unsigned uSeqCount = a.GetSeqCount();
                       ^
profilefrommsa.cpp:253:11: warning: unused variable 'uHydrophobicRunLength' [-Wunused-variable]
        unsigned uHydrophobicRunLength = 0;
                 ^
In file included from profilefrommsa.cpp:1:
In file included from ./muscle.h:38:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
profilefrommsa.cpp:15:20: warning: unused function 'LocalScoreToStr' [-Wunused-function]
static const char *LocalScoreToStr(SCORE s)
                   ^
5 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c progalign.cpp -o progalign.o
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)
              ^
2 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c progress.cpp -o progress.o
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)
              ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c progressivealign.cpp -o progressivealign.o
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)
              ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c pwpath.cpp -o pwpath.o
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)
              ^
3 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c readmx.cpp -o readmx.o
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)
                ^
2 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c realigndiffs.cpp -o realigndiffs.o
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)
              ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c realigndiffse.cpp -o realigndiffse.o
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)
              ^
3 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c refine.cpp -o refine.o
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)
                       ^
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)
              ^
2 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c refinehoriz.cpp -o refinehoriz.o
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)
              ^
2 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c refinesubfams.cpp -o refinesubfams.o
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)
              ^
2 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c refinetree.cpp -o refinetree.o
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)
              ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c refinetreee.cpp -o refinetreee.o
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)
              ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c refinevert.cpp -o refinevert.o
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)
              ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c refinew.cpp -o refinew.o
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)
              ^
3 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c savebest.cpp -o savebest.o
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)
              ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c scoredist.cpp -o scoredist.o
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;
                    ^
3 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c scoregaps.cpp -o scoregaps.o
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)
             ^
3 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c scorehistory.cpp -o scorehistory.o
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)
              ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c scorepp.cpp -o scorepp.o
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)
              ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c seq.cpp -o seq.o
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)
              ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c seqvect.cpp -o seqvect.o
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;
             ^
3 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c setblosumweights.cpp -o setblosumweights.o
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)
              ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c setgscweights.cpp -o setgscweights.o
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)
              ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c setnewhandler.cpp -o setnewhandler.o
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)
              ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c spfast.cpp -o spfast.o
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)
             ^
4 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c sptest.cpp -o sptest.o
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)
              ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c stabilize.cpp -o stabilize.o
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)
              ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c subfam.cpp -o subfam.o
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)
              ^
2 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c subfams.cpp -o subfams.o
subfams.cpp:44:25: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
        for (unsigned i = 0; i < uNodeCount; ++i)
                             ~ ^ ~~~~~~~~~~
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:10:13: warning: unused function 'GetMostDistantPair' [-Wunused-function]
static void GetMostDistantPair(DistFunc &DF, unsigned *ptrIndex1, unsigned *ptrIndex2)
            ^
subfams.cpp:40:13: warning: unused function 'InitializeSingleSource' [-Wunused-function]
static void InitializeSingleSource(DistFunc &DF, unsigned uIndex)
            ^
subfams.cpp:52:13: warning: unused function 'Relax' [-Wunused-function]
static void Relax(DistFunc &DF, unsigned u, unsigned v)
            ^
5 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c sw.cpp -o sw.o
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,
            ^
2 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c termgaps.cpp -o termgaps.o
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)
              ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c textfile.cpp -o textfile.o
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)
              ^
3 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c threewaywt.cpp -o threewaywt.o
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)
              ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c tomhydro.cpp -o tomhydro.o
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)
              ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c traceback.cpp -o traceback.o
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)
              ^
6 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c tracebackopt.cpp -o tracebackopt.o
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)
              ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c tracebacksw.cpp -o tracebacksw.o
tracebacksw.cpp:22:17: warning: unused variable 'uPrefixCountB' [-Wunused-variable]
        const unsigned uPrefixCountB = uLengthB + 1;
                       ^
tracebacksw.cpp:29:8: warning: unused variable 'scoreMax' [-Wunused-variable]
        SCORE scoreMax = DPM(uPrefixLengthA, uPrefixLengthB);
              ^
tracebacksw.cpp:175:3: warning: variable 'cPrevEdgeType' is used uninitialized whenever switch default is taken [-Wsometimes-uninitialized]
                default:
                ^~~~~~~
tracebacksw.cpp:182:15: note: uninitialized use occurs here
                cEdgeType = cPrevEdgeType;
                            ^~~~~~~~~~~~~
tracebacksw.cpp:166:13: warning: variable 'cPrevEdgeType' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
                        else if (EQ(Score, scoreSI))
                                 ^~~~~~~~~~~~~~~~~~
tracebacksw.cpp:8:18: note: expanded from macro 'EQ'
#define EQ(a, b)        (fabs(a-b) < 0.1)
                        ^~~~~~~~~~~~~~~~~
tracebacksw.cpp:182:15: note: uninitialized use occurs here
                cEdgeType = cPrevEdgeType;
                            ^~~~~~~~~~~~~
tracebacksw.cpp:166:9: note: remove the 'if' if its condition is always true
                        else if (EQ(Score, scoreSI))
                             ^~~~~~~~~~~~~~~~~~~~~~~
tracebacksw.cpp:130:13: warning: variable 'cPrevEdgeType' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
                        else if (EQ(Score, scoreSD))
                                 ^~~~~~~~~~~~~~~~~~
tracebacksw.cpp:8:18: note: expanded from macro 'EQ'
#define EQ(a, b)        (fabs(a-b) < 0.1)
                        ^~~~~~~~~~~~~~~~~
tracebacksw.cpp:182:15: note: uninitialized use occurs here
                cEdgeType = cPrevEdgeType;
                            ^~~~~~~~~~~~~
tracebacksw.cpp:130:9: note: remove the 'if' if its condition is always true
                        else if (EQ(Score, scoreSD))
                             ^~~~~~~~~~~~~~~~~~~~~~~
tracebacksw.cpp:92:13: warning: variable 'cPrevEdgeType' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
                        else if (EQ(scoreMatch, Score))
                                 ^~~~~~~~~~~~~~~~~~~~~
tracebacksw.cpp:8:18: note: expanded from macro 'EQ'
#define EQ(a, b)        (fabs(a-b) < 0.1)
                        ^~~~~~~~~~~~~~~~~
tracebacksw.cpp:182:15: note: uninitialized use occurs here
                cEdgeType = cPrevEdgeType;
                            ^~~~~~~~~~~~~
tracebacksw.cpp:92:9: note: remove the 'if' if its condition is always true
                        else if (EQ(scoreMatch, Score))
                             ^~~~~~~~~~~~~~~~~~~~~~~~~~
tracebacksw.cpp:43:21: note: initialize the variable 'cPrevEdgeType' to silence this warning
                char cPrevEdgeType;
                                  ^
                                   = '\0'
In file included from tracebacksw.cpp:1:
In file included from ./muscle.h:38:
./intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function]
static double ScoreToDouble(SCORE Score)
              ^
7 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c treefrommsa.cpp -o treefrommsa.o
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)
                       ^
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)
              ^
2 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c typetostr.cpp -o typetostr.o
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)
              ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c upgma2.cpp -o upgma2.o
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()
            ^
8 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c usage.cpp -o usage.o
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)
              ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c validateids.cpp -o validateids.o
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)
              ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c vtml2.cpp -o vtml2.o
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)
              ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c writescorefile.cpp -o writescorefile.o
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)
              ^
2 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c RMuscle.cpp -o RMuscle.o
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)
              ^
1 warning generated.
clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/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 -I. "; \
	/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... i386-apple-darwin15.6.0
checking host system type... i386-apple-darwin15.6.0
checking target system type... i386-apple-darwin15.6.0
building for darwin15.6.0
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... yes
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
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -DHAVE_CONFIG_H -I.  -fPIC  -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:42:
In file included from pairwise/../alignment/../substitutionMatrix/globalmatrix.h:8:
pairwise/../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
        void printInFormat(vector& temp, char* name = "tempfile.out");
                                                             ^
pairwise/../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
        void printVectorToFile(vector& temp, char* name = "tempfile.out");
                                                                 ^
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;
            ^
5 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -DHAVE_CONFIG_H -I.  -fPIC  -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:42:
In file included from pairwise/../alignment/../substitutionMatrix/globalmatrix.h:8:
pairwise/../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
        void printInFormat(vector& temp, char* name = "tempfile.out");
                                                             ^
pairwise/../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
        void printVectorToFile(vector& temp, char* name = "tempfile.out");
                                                                 ^
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;
            ^
5 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -DHAVE_CONFIG_H -I.  -fPIC  -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++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -DHAVE_CONFIG_H -I.  -fPIC  -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();
               ^
In file included from fileInput/FileReader.cpp:29:
In file included from fileInput/FileReader.h:12:
In file included from fileInput/../alignment/Alignment.h:42:
In file included from fileInput/../alignment/../substitutionMatrix/globalmatrix.h:8:
fileInput/../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
        void printInFormat(vector& temp, char* name = "tempfile.out");
                                                             ^
fileInput/../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
        void printVectorToFile(vector& temp, char* name = "tempfile.out");
                                                                 ^
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;
            ^
5 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -DHAVE_CONFIG_H -I.  -fPIC  -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++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -DHAVE_CONFIG_H -I.  -fPIC  -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++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -DHAVE_CONFIG_H -I.  -fPIC  -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++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -DHAVE_CONFIG_H -I.  -fPIC  -Wall -g -O2  -c fileInput/InFileStream.cpp -o fileInput/InFileStream.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -DHAVE_CONFIG_H -I.  -fPIC  -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++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -DHAVE_CONFIG_H -I.  -fPIC  -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++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -DHAVE_CONFIG_H -I.  -fPIC  -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();
                    ^
fileInput/FileParser.cpp:56:5: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
    register int i;
    ^~~~~~~~~
fileInput/FileParser.cpp:57:5: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
    register char c;
    ^~~~~~~~~
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;
            ^
6 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -DHAVE_CONFIG_H -I.  -fPIC  -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++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -DHAVE_CONFIG_H -I.  -fPIC  -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:42:
In file included from tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h:8:
tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
        void printInFormat(vector& temp, char* name = "tempfile.out");
                                                             ^
tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
        void printVectorToFile(vector& temp, char* name = "tempfile.out");
                                                                 ^
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;
            ^
5 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -DHAVE_CONFIG_H -I.  -fPIC  -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:8:
In file included from tree/UPGMA/RootedGuideTree.h:17:
In file included from tree/UPGMA/../../alignment/Alignment.h:42:
In file included from tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h:8:
tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
        void printInFormat(vector& temp, char* name = "tempfile.out");
                                                             ^
tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
        void printVectorToFile(vector& temp, char* name = "tempfile.out");
                                                                 ^
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;
            ^
5 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -DHAVE_CONFIG_H -I.  -fPIC  -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++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -DHAVE_CONFIG_H -I.  -fPIC  -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:42:
In file included from tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h:8:
tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
        void printInFormat(vector& temp, char* name = "tempfile.out");
                                                             ^
tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
        void printVectorToFile(vector& temp, char* name = "tempfile.out");
                                                                 ^
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;
            ^
5 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -DHAVE_CONFIG_H -I.  -fPIC  -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:42:
In file included from tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h:8:
tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
        void printInFormat(vector& temp, char* name = "tempfile.out");
                                                             ^
tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
        void printVectorToFile(vector& temp, char* name = "tempfile.out");
                                                                 ^
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;
            ^
5 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -DHAVE_CONFIG_H -I.  -fPIC  -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:42:
In file included from tree/../alignment/../substitutionMatrix/globalmatrix.h:8:
tree/../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
        void printInFormat(vector& temp, char* name = "tempfile.out");
                                                             ^
tree/../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
        void printVectorToFile(vector& temp, char* name = "tempfile.out");
                                                                 ^
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;
            ^
5 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -DHAVE_CONFIG_H -I.  -fPIC  -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();
               ^
In file included from tree/ClusterTree.cpp:9:
In file included from tree/ClusterTree.h:20:
In file included from tree/../alignment/Alignment.h:42:
In file included from tree/../alignment/../substitutionMatrix/globalmatrix.h:8:
tree/../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
        void printInFormat(vector& temp, char* name = "tempfile.out");
                                                             ^
tree/../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
        void printVectorToFile(vector& temp, char* name = "tempfile.out");
                                                                 ^
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++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -DHAVE_CONFIG_H -I.  -fPIC  -Wall -g -O2  -c tree/TreeInterface.cpp -o tree/TreeInterface.o
In file included from tree/TreeInterface.cpp:15:
In file included from tree/TreeInterface.h:19:
In file included from tree/../alignment/Alignment.h:41:
In file included from tree/../alignment/Sequence.h:20:
In file included from tree/../alignment/../general/userparams.h:8:
In file included from tree/../alignment/../general/UserParameters.h:22:
In file included from tree/../alignment/../general/utils.h:8:
In file included from tree/../alignment/../general/Utility.h:15:
In file included from tree/../alignment/../general/clustalw.h:42:
tree/../alignment/../general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable]
           int y = x.size();
               ^
In file included from tree/TreeInterface.cpp:15:
In file included from tree/TreeInterface.h:19:
In file included from tree/../alignment/Alignment.h:41:
In file included from tree/../alignment/Sequence.h:20:
In file included from tree/../alignment/../general/userparams.h:8:
In file included from tree/../alignment/../general/UserParameters.h:22:
In file included from tree/../alignment/../general/utils.h:8:
In file included from tree/../alignment/../general/Utility.h:15:
In file included from tree/../alignment/../general/clustalw.h:43:
tree/../alignment/../general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable]
           int y = x.size();
               ^
In file included from tree/TreeInterface.cpp:15:
In file included from tree/TreeInterface.h:19:
In file included from tree/../alignment/Alignment.h:42:
In file included from tree/../alignment/../substitutionMatrix/globalmatrix.h:8:
tree/../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
        void printInFormat(vector& temp, char* name = "tempfile.out");
                                                             ^
tree/../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
        void printVectorToFile(vector& temp, char* name = "tempfile.out");
                                                                 ^
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;
            ^
5 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -DHAVE_CONFIG_H -I.  -fPIC  -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:42:
In file included from tree/../alignment/../substitutionMatrix/globalmatrix.h:8:
tree/../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
        void printInFormat(vector& temp, char* name = "tempfile.out");
                                                             ^
tree/../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
        void printVectorToFile(vector& temp, char* name = "tempfile.out");
                                                                 ^
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;
            ^
5 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -DHAVE_CONFIG_H -I.  -fPIC  -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:42:
In file included from tree/../alignment/../substitutionMatrix/globalmatrix.h:8:
tree/../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
        void printInFormat(vector& temp, char* name = "tempfile.out");
                                                             ^
tree/../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
        void printVectorToFile(vector& temp, char* name = "tempfile.out");
                                                                 ^
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;
            ^
5 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -DHAVE_CONFIG_H -I.  -fPIC  -Wall -g -O2  -c tree/RandomGenerator.cpp -o tree/RandomGenerator.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -DHAVE_CONFIG_H -I.  -fPIC  -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();
               ^
tree/NJTree.cpp:164:5: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
    register int i;
    ^~~~~~~~~
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;
            ^
4 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -DHAVE_CONFIG_H -I.  -fPIC  -Wall -g -O2  -c tree/AlignmentSteps.cpp -o tree/AlignmentSteps.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -DHAVE_CONFIG_H -I.  -fPIC  -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:18:
In file included from ./fileInput/FileReader.h:12:
In file included from ./fileInput/../alignment/Alignment.h:42:
In file included from ./fileInput/../alignment/../substitutionMatrix/globalmatrix.h:8:
./fileInput/../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
        void printInFormat(vector& temp, char* name = "tempfile.out");
                                                             ^
./fileInput/../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
        void printVectorToFile(vector& temp, char* name = "tempfile.out");
                                                                 ^
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;
            ^
5 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -DHAVE_CONFIG_H -I.  -fPIC  -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();
               ^
In file included from substitutionMatrix/SubMatrix.cpp:15:
substitutionMatrix/SubMatrix.h:106:62: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
        void printInFormat(vector& temp, char* name = "tempfile.out");
                                                             ^
substitutionMatrix/SubMatrix.h:107:66: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
        void printVectorToFile(vector& temp, char* name = "tempfile.out");
                                                                 ^
substitutionMatrix/SubMatrix.cpp:1308:12: warning: unused variable 'llimit' [-Wunused-variable]
    int n, llimit, ulimit;
           ^
substitutionMatrix/SubMatrix.cpp:1308:20: warning: unused variable 'ulimit' [-Wunused-variable]
    int n, llimit, ulimit;
                   ^
substitutionMatrix/SubMatrix.cpp:1307:9: warning: unused variable 'nmat' [-Wunused-variable]
    int nmat;
        ^
substitutionMatrix/SubMatrix.cpp:1305:10: warning: unused variable 'inline1' [-Wunused-variable]
    char inline1[1024];
         ^
substitutionMatrix/SubMatrix.cpp:1308:9: warning: unused variable 'n' [-Wunused-variable]
    int n, llimit, ulimit;
        ^
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;
            ^
10 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -DHAVE_CONFIG_H -I.  -fPIC  -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();
               ^
In file included from multipleAlign/Iteration.cpp:13:
In file included from multipleAlign/Iteration.h:8:
In file included from multipleAlign/../alignment/Alignment.h:42:
In file included from multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8:
multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
        void printInFormat(vector& temp, char* name = "tempfile.out");
                                                             ^
multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
        void printVectorToFile(vector& temp, char* name = "tempfile.out");
                                                                 ^
multipleAlign/Iteration.cpp:231:17: warning: 'tmpnam' is deprecated: This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of tmpnam(3), it is highly recommended that you use mkstemp(3) instead. [-Wdeprecated-declarations]
                tmpnam (buffer);
                ^
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:277:7: note: 'tmpnam' has been explicitly marked deprecated here
char    *tmpnam(char *);
         ^
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;
            ^
6 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -DHAVE_CONFIG_H -I.  -fPIC  -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();
               ^
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:42:
In file included from multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8:
multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
        void printInFormat(vector& temp, char* name = "tempfile.out");
                                                             ^
multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
        void printVectorToFile(vector& temp, char* name = "tempfile.out");
                                                                 ^
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;
            ^
6 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -DHAVE_CONFIG_H -I.  -fPIC  -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:42:
In file included from multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8:
multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
        void printInFormat(vector& temp, char* name = "tempfile.out");
                                                             ^
multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
        void printVectorToFile(vector& temp, char* name = "tempfile.out");
                                                                 ^
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];
            ^
6 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -DHAVE_CONFIG_H -I.  -fPIC  -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:42:
In file included from multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8:
multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
        void printInFormat(vector& temp, char* name = "tempfile.out");
                                                             ^
multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
        void printVectorToFile(vector& temp, char* name = "tempfile.out");
                                                                 ^
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;
            ^
5 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -DHAVE_CONFIG_H -I.  -fPIC  -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:42:
In file included from multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8:
multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
        void printInFormat(vector& temp, char* name = "tempfile.out");
                                                             ^
multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
        void printVectorToFile(vector& temp, char* name = "tempfile.out");
                                                                 ^
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;
            ^
5 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -DHAVE_CONFIG_H -I.  -fPIC  -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:42:
In file included from multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8:
multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
        void printInFormat(vector& temp, char* name = "tempfile.out");
                                                             ^
multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
        void printVectorToFile(vector& temp, char* name = "tempfile.out");
                                                                 ^
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;
            ^
5 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -DHAVE_CONFIG_H -I.  -fPIC  -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:42:
In file included from multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8:
multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
        void printInFormat(vector& temp, char* name = "tempfile.out");
                                                             ^
multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
        void printVectorToFile(vector& temp, char* name = "tempfile.out");
                                                                 ^
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;
            ^
5 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -DHAVE_CONFIG_H -I.  -fPIC  -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++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -DHAVE_CONFIG_H -I.  -fPIC  -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();
               ^
general/UserParameters.cpp:475:5: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
    register int i;
    ^~~~~~~~~
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;
            ^
4 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -DHAVE_CONFIG_H -I.  -fPIC  -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:53:5: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
    register int p;
    ^~~~~~~~~
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++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -DHAVE_CONFIG_H -I.  -fPIC  -Wall -g -O2  -c general/InvalidCombination.cpp -o general/InvalidCombination.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -DHAVE_CONFIG_H -I.  -fPIC  -Wall -g -O2  -c general/DebugLog.cpp -o general/DebugLog.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -DHAVE_CONFIG_H -I.  -fPIC  -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();
               ^
general/ClustalWResources.cpp:106:5: warning: array index 1 is past the end of the array (which contains 1 element) [-Warray-bounds]
    delim[1] = 0;
    ^     ~
general/ClustalWResources.cpp:104:5: note: array 'delim' declared here
    char delim[1];
    ^
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;
            ^
4 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -DHAVE_CONFIG_H -I.  -fPIC  -Wall -g -O2  -c general/VectorOutOfRange.cpp -o general/VectorOutOfRange.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -DHAVE_CONFIG_H -I.  -fPIC  -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++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -DHAVE_CONFIG_H -I.  -fPIC  -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:42:
In file included from general/../alignment/../substitutionMatrix/globalmatrix.h:8:
general/../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
        void printInFormat(vector& temp, char* name = "tempfile.out");
                                                             ^
general/../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
        void printVectorToFile(vector& temp, char* name = "tempfile.out");
                                                                 ^
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;
            ^
5 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -DHAVE_CONFIG_H -I.  -fPIC  -Wall -g -O2  -c Help.cpp -o Help.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -DHAVE_CONFIG_H -I.  -fPIC  -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();
               ^
In file included from alignment/Alignment.cpp:25:
In file included from alignment/Alignment.h:42:
In file included from alignment/../substitutionMatrix/globalmatrix.h:8:
alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
        void printInFormat(vector& temp, char* name = "tempfile.out");
                                                             ^
alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
        void printVectorToFile(vector& temp, char* name = "tempfile.out");
                                                                 ^
alignment/Alignment.cpp:47:5: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
    register int sl;                /* which have  code = gap_pos2  */
    ^~~~~~~~~
alignment/Alignment.cpp:122:5: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
    register int sl;                /* which have  code = gap_pos2  */
    ^~~~~~~~~
alignment/Alignment.cpp:617:5: warning: 'register' storage class specifier is deprecated and incompatible with C++1z [-Wdeprecated-register]
    register int sl;
    ^~~~~~~~~
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;
            ^
9 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -DHAVE_CONFIG_H -I.  -fPIC  -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:42:
In file included from alignment/../substitutionMatrix/globalmatrix.h:8:
alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
        void printInFormat(vector& temp, char* name = "tempfile.out");
                                                             ^
alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
        void printVectorToFile(vector& temp, char* name = "tempfile.out");
                                                                 ^
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;
            ^
5 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -DHAVE_CONFIG_H -I.  -fPIC  -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:15:
In file included from alignment/../substitutionMatrix/globalmatrix.h:8:
alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
        void printInFormat(vector& temp, char* name = "tempfile.out");
                                                             ^
alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
        void printVectorToFile(vector& temp, char* name = "tempfile.out");
                                                                 ^
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;
                       ^
9 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -DHAVE_CONFIG_H -I.  -fPIC  -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++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -DHAVE_CONFIG_H -I.  -fPIC  -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:18:
In file included from ./fileInput/FileReader.h:12:
In file included from ./fileInput/../alignment/Alignment.h:42:
In file included from ./fileInput/../alignment/../substitutionMatrix/globalmatrix.h:8:
./fileInput/../alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
        void printInFormat(vector& temp, char* name = "tempfile.out");
                                                             ^
./fileInput/../alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
        void printVectorToFile(vector& temp, char* name = "tempfile.out");
                                                                 ^
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;
            ^
5 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -DHAVE_CONFIG_H -I.  -fPIC  -Wall -g -O2  -c RClustalWMain.cpp -o RClustalWMain.o
In file included from RClustalWMain.cpp:5:
In file included from ./alignment/Alignment.h:41:
In file included from ./alignment/Sequence.h:20:
In file included from ./alignment/../general/userparams.h:8:
In file included from ./alignment/../general/UserParameters.h:22:
In file included from ./alignment/../general/utils.h:8:
In file included from ./alignment/../general/Utility.h:15:
In file included from ./alignment/../general/clustalw.h:42:
./alignment/../general/Array2D.h:28:16: warning: unused variable 'y' [-Wunused-variable]
           int y = x.size();
               ^
In file included from RClustalWMain.cpp:5:
In file included from ./alignment/Alignment.h:41:
In file included from ./alignment/Sequence.h:20:
In file included from ./alignment/../general/userparams.h:8:
In file included from ./alignment/../general/UserParameters.h:22:
In file included from ./alignment/../general/utils.h:8:
In file included from ./alignment/../general/Utility.h:15:
In file included from ./alignment/../general/clustalw.h:43:
./alignment/../general/SquareMat.h:26:16: warning: unused variable 'y' [-Wunused-variable]
           int y = x.size();
               ^
In file included from RClustalWMain.cpp:5:
In file included from ./alignment/Alignment.h:42:
In file included from ./alignment/../substitutionMatrix/globalmatrix.h:8:
./alignment/../substitutionMatrix/SubMatrix.h:106:62: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
        void printInFormat(vector& temp, char* name = "tempfile.out");
                                                             ^
./alignment/../substitutionMatrix/SubMatrix.h:107:66: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
        void printVectorToFile(vector& temp, char* name = "tempfile.out");
                                                                 ^
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;
            ^
5 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -DHAVE_CONFIG_H -I.  -fPIC  -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++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/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-7.2/include"; \
	export PKG_CFLAGS="  -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include"; \
	cd src; \
	/Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB -o libClustalOmega.so exceptions4c/e4c_lite.c argtable2/argtable2.c argtable2/arg_end.c argtable2/arg_rem.c argtable2/arg_lit.c argtable2/arg_int.c argtable2/arg_dbl.c argtable2/arg_str.c argtable2/arg_file.c kmpp/KMeans.cpp kmpp/KmTree.cpp kmpp/KmUtils.cpp clustal/hhalign_wrapper.c clustal/ktuple_pair.c clustal/list.c clustal/log.c clustal/muscle_upgma.c clustal/muscle_tree.c clustal/mbed.c clustal/pair_dist.c clustal/progress.c clustal/seq.c clustal/symmatrix.c clustal/tree.c clustal/util.c clustal/weights.c squid/a2m.c squid/aligneval.c squid/alignio.c squid/clustal.c squid/cluster.c squid/dayhoff.c squid/eps.c squid/file.c squid/getopt.c squid/gki.c squid/gsi.c squid/gsi64.c squid/hsregex.c squid/iupac.c squid/msa.c squid/msf.c squid/phylip.c squid/revcomp.c squid/rk.c squid/selex.c squid/seqencode.c squid/shuffle.c squid/sqerror.c squid/sqio.c squid/squidcore.c squid/sre_ctype.c squid/sre_math.c squid/sre_random.c squid/sre_string.c squid/ssi.c squid/stack.c squid/stockholm.c squid/stopwatch.c squid/translate.c squid/types.c squid/vectorops.c squid/weight.c hhalign/hhalign.cpp RClustalOmega.cpp mymain.c clustal-omega.c && \
	ar rcs libClustalOmega.a exceptions4c/e4c_lite.o argtable2/argtable2.o argtable2/arg_end.o argtable2/arg_rem.o argtable2/arg_lit.o argtable2/arg_int.o argtable2/arg_dbl.o argtable2/arg_str.o argtable2/arg_file.o kmpp/KMeans.o kmpp/KmTree.o kmpp/KmUtils.o clustal/hhalign_wrapper.o clustal/ktuple_pair.o clustal/list.o clustal/log.o clustal/muscle_upgma.o clustal/muscle_tree.o clustal/mbed.o clustal/pair_dist.o clustal/progress.o clustal/seq.o clustal/symmatrix.o clustal/tree.o clustal/util.o clustal/weights.o squid/a2m.o squid/aligneval.o squid/alignio.o squid/clustal.o squid/cluster.o squid/dayhoff.o squid/eps.o squid/file.o squid/getopt.o squid/gki.o squid/gsi.o squid/gsi64.o squid/hsregex.o squid/iupac.o squid/msa.o squid/msf.o squid/phylip.o squid/revcomp.o squid/rk.o squid/selex.o squid/seqencode.o squid/shuffle.o squid/sqerror.o squid/sqio.o squid/squidcore.o squid/sre_ctype.o squid/sre_math.o squid/sre_random.o squid/sre_string.o squid/ssi.o squid/stack.o squid/stockholm.o squid/stopwatch.o squid/translate.o squid/types.o squid/vectorops.o squid/weight.o hhalign/hhalign.o RClustalOmega.o mymain.o clustal-omega.o && \
	cp libClustalOmega.a ../../
configure:

    Welcome to Clustal Omega - version 1.2.0 (AndreaGiacomo)

                       +NMMMMMMMMMS=
                    MMMMM?      :MMMMM8
                  IMMMMS           MMMMM,
                ~MMMMN              ,MMMMM
               =MMMMM                 MMMMM
              ?MMMMM                  +MMMMM
              MMMMMS                   MMMMM
              MMMMM                    MMMMM:
              MMMMM                    MMMMM+
              MMMMM                    MMMMM~
              MMMMM                    MMMMM
              MMMMMZ                   MMMMM
               MMMMM                  ,MMMMZ
                MMMM8                 MMMM+
                 MMMMS               MMMM,
                   MMMMO           MMMM
            ,N       SMMM        MMM8       +8
            ,M7         M+       M+        :M8
            ,MMMMMMMMMMMMI       MMMMMMMMMMMM8
            ,MMMMMMMMMMMM8       MMMMMMMMMMMM8
            ,MMMMMMMMMMMMN       MMMMMMMMMMMM8

              
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... ./install-sh -c -d
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checking whether make sets $(MAKE)... yes
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checking for gcc... gcc
checking whether the C compiler works... yes
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checking for suffix of executables... 
checking whether we are cross compiling... no
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checking whether we are using the GNU C compiler... yes
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checking dependency style of gcc... gcc3
checking how to run the C preprocessor... gcc -E
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checking build system type... i386-apple-darwin15.6.0
checking host system type... i386-apple-darwin15.6.0
checking whether make sets $(MAKE)... (cached) yes
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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... 196608
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
checking for /Library/Developer/CommandLineTools/usr/bin/ld option to reload object files... -r
checking for objdump... no
checking how to recognize dependent libraries... pass_all
checking for ar... ar
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checking command to parse /usr/bin/nm -B output from gcc object... ok
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checking if gcc PIC flag -fno-common -DPIC works... yes
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checking whether the gcc linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... darwin15.6.0 dyld
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
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checking for gcc... (cached) gcc
checking whether we are using the GNU C compiler... (cached) yes
checking whether gcc accepts -g... (cached) yes
checking for gcc option to accept ISO C89... (cached) none needed
checking dependency style of gcc... (cached) gcc3
checking how to run the C preprocessor... gcc -E
checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking dependency style of g++... gcc3
checking whether we are using the GNU C++ compiler... (cached) yes
checking whether g++ accepts -g... (cached) yes
checking dependency style of g++... (cached) gcc3
checking how to run the C++ preprocessor... g++ -E
checking for ld used by g++... /Library/Developer/CommandLineTools/usr/bin/ld
checking if the linker (/Library/Developer/CommandLineTools/usr/bin/ld) is GNU ld... no
checking whether the g++ linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes
checking for g++ option to produce PIC... -fno-common -DPIC
checking if g++ PIC flag -fno-common -DPIC works... yes
checking if g++ static flag -static works... no
checking if g++ supports -c -o file.o... yes
checking if g++ supports -c -o file.o... (cached) yes
checking whether the g++ linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... darwin15.6.0 dyld
checking how to hardcode library paths into programs... immediate
checking how to run the C++ preprocessor... g++ -E
checking for ANSI C header files... (cached) yes
checking assert.h usability... yes
checking assert.h presence... yes
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checking ctype.h usability... yes
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checking float.h usability... yes
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checking limits.h usability... yes
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checking math.h usability... yes
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checking size of unsigned short... 2
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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: executing depfiles commands
config.status: executing libtool commands
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC  -Wall -g -O2  -c exceptions4c/e4c_lite.c -o exceptions4c/e4c_lite.o
exceptions4c/e4c_lite.c:16:27: warning: suggest braces around initialization of subobject [-Wmissing-braces]
struct e4c_context e4c = {0};
                          ^
                          {}
exceptions4c/e4c_lite.c:16:27: warning: suggest braces around initialization of subobject [-Wmissing-braces]
struct e4c_context e4c = {0};
                          ^
                          {}
2 warnings generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC  -Wall -g -O2  -c argtable2/argtable2.c -o argtable2/argtable2.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC  -Wall -g -O2  -c argtable2/arg_end.c -o argtable2/arg_end.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC  -Wall -g -O2  -c argtable2/arg_rem.c -o argtable2/arg_rem.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC  -Wall -g -O2  -c argtable2/arg_lit.c -o argtable2/arg_lit.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC  -Wall -g -O2  -c argtable2/arg_int.c -o argtable2/arg_int.o
argtable2/arg_int.c:60:12: warning: implicitly declaring library function 'isspace' with type 'int (int)' [-Wimplicit-function-declaration]
    while (isspace(*ptr))
           ^
argtable2/arg_int.c:60:12: note: include the header  or explicitly provide a declaration for 'isspace'
argtable2/arg_int.c:89:8: warning: implicitly declaring library function 'toupper' with type 'int (int)' [-Wimplicit-function-declaration]
   if (toupper(*ptr++)!=toupper(X))
       ^
argtable2/arg_int.c:89:8: note: include the header  or explicitly provide a declaration for 'toupper'
2 warnings generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC  -Wall -g -O2  -c argtable2/arg_dbl.c -o argtable2/arg_dbl.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC  -Wall -g -O2  -c argtable2/arg_str.c -o argtable2/arg_str.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC  -Wall -g -O2  -c argtable2/arg_file.c -o argtable2/arg_file.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -DMATH_H_CLIB -std=c++98 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC  -Wall -g -O2  -c kmpp/KMeans.cpp -o kmpp/KMeans.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -DMATH_H_CLIB -std=c++98 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC  -Wall -g -O2  -c kmpp/KmTree.cpp -o kmpp/KmTree.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -DMATH_H_CLIB -std=c++98 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC  -Wall -g -O2  -c kmpp/KmUtils.cpp -o kmpp/KmUtils.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC  -Wall -g -O2  -c clustal/hhalign_wrapper.c -o clustal/hhalign_wrapper.o
In file included from clustal/hhalign_wrapper.c:22:
./config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined]
#define NDEBUG /**/
        ^
:1:9: note: previous definition is here
#define NDEBUG 1
        ^
clustal/hhalign_wrapper.c:84:9: warning: unused variable 'iR' [-Wunused-variable]
    int iR; /* iterator for residue */
        ^
clustal/hhalign_wrapper.c:85:9: warning: unused variable 'iLen' [-Wunused-variable]
    int iLen; /* length of sequence */
        ^
3 warnings generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC  -Wall -g -O2  -c clustal/ktuple_pair.c -o clustal/ktuple_pair.o
In file included from clustal/ktuple_pair.c:29:
./config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined]
#define NDEBUG /**/
        ^
:1:9: note: previous definition is here
#define NDEBUG 1
        ^
1 warning generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC  -Wall -g -O2  -c clustal/list.c -o clustal/list.o
In file included from clustal/list.c:32:
./config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined]
#define NDEBUG /**/
        ^
:1:9: note: previous definition is here
#define NDEBUG 1
        ^
1 warning generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC  -Wall -g -O2  -c clustal/log.c -o clustal/log.o
In file included from clustal/log.c:22:
./config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined]
#define NDEBUG /**/
        ^
:1:9: note: previous definition is here
#define NDEBUG 1
        ^
1 warning generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC  -Wall -g -O2  -c clustal/muscle_upgma.c -o clustal/muscle_upgma.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC  -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 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC  -Wall -g -O2  -c clustal/mbed.c -o clustal/mbed.o
In file included from clustal/mbed.c:28:
./config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined]
#define NDEBUG /**/
        ^
:1:9: note: previous definition is here
#define NDEBUG 1
        ^
clustal/mbed.c:69:18: warning: unused variable 'MAX_ALLOWED_SEQ_PER_PRECLUSTER' [-Wunused-const-variable]
static const int MAX_ALLOWED_SEQ_PER_PRECLUSTER = 100;
                 ^
2 warnings generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC  -Wall -g -O2  -c clustal/pair_dist.c -o clustal/pair_dist.o
In file included from clustal/pair_dist.c:22:
./config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined]
#define NDEBUG /**/
        ^
:1:9: note: previous definition is here
#define NDEBUG 1
        ^
clustal/pair_dist.c:177:10: warning: unused variable 'bPrintCR' [-Wunused-variable]
    bool bPrintCR = (rLog.iLogLevelEnabled<=LOG_VERBOSE) ? FALSE : TRUE;
         ^
2 warnings generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC  -Wall -g -O2  -c clustal/progress.c -o clustal/progress.o
In file included from clustal/progress.c:22:
./config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined]
#define NDEBUG /**/
        ^
:1:9: note: previous definition is here
#define NDEBUG 1
        ^
1 warning generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC  -Wall -g -O2  -c clustal/seq.c -o clustal/seq.o
In file included from clustal/seq.c:30:
./config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined]
#define NDEBUG /**/
        ^
:1:9: note: previous definition is here
#define NDEBUG 1
        ^
clustal/seq.c:68:9: warning: unused variable 'iAux' [-Wunused-variable]
    int iAux;
        ^
2 warnings generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC  -Wall -g -O2  -c clustal/symmatrix.c -o clustal/symmatrix.o
In file included from clustal/symmatrix.c:30:
./config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined]
#define NDEBUG /**/
        ^
:1:9: note: previous definition is here
#define NDEBUG 1
        ^
1 warning generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC  -Wall -g -O2  -c clustal/tree.c -o clustal/tree.o
In file included from clustal/tree.c:22:
./config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined]
#define NDEBUG /**/
        ^
:1:9: note: previous definition is here
#define NDEBUG 1
        ^
1 warning generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC  -Wall -g -O2  -c clustal/util.c -o clustal/util.o
In file included from clustal/util.c:22:
./config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined]
#define NDEBUG /**/
        ^
:1:9: note: previous definition is here
#define NDEBUG 1
        ^
1 warning generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC  -Wall -g -O2  -c clustal/weights.c -o clustal/weights.o
In file included from clustal/weights.c:72:
./config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined]
#define NDEBUG /**/
        ^
:1:9: note: previous definition is here
#define NDEBUG 1
        ^
1 warning generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC  -Wall -g -O2  -c squid/a2m.c -o squid/a2m.o
In file included from squid/a2m.c:20:
In file included from squid/squid.h:32:
squid/../config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined]
#define NDEBUG /**/
        ^
:1:9: note: previous definition is here
#define NDEBUG 1
        ^
1 warning generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC  -Wall -g -O2  -c squid/aligneval.c -o squid/aligneval.o
In file included from squid/aligneval.c:59:
In file included from squid/squid.h:32:
squid/../config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined]
#define NDEBUG /**/
        ^
:1:9: note: previous definition is here
#define NDEBUG 1
        ^
1 warning generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC  -Wall -g -O2  -c squid/alignio.c -o squid/alignio.o
In file included from squid/alignio.c:21:
In file included from squid/squid.h:32:
squid/../config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined]
#define NDEBUG /**/
        ^
:1:9: note: previous definition is here
#define NDEBUG 1
        ^
1 warning generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC  -Wall -g -O2  -c squid/clustal.c -o squid/clustal.o
In file included from squid/clustal.c:24:
In file included from squid/squid.h:32:
squid/../config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined]
#define NDEBUG /**/
        ^
:1:9: note: previous definition is here
#define NDEBUG 1
        ^
squid/clustal.c:214:7: warning: unused variable 'cons' [-Wunused-variable]
  int cons;
      ^
squid/clustal.c:438:6: warning: unused variable 'cons' [-Wunused-variable]
        int cons;
            ^
3 warnings generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC  -Wall -g -O2  -c squid/cluster.c -o squid/cluster.o
In file included from squid/cluster.c:124:
In file included from squid/squid.h:32:
squid/../config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined]
#define NDEBUG /**/
        ^
:1:9: note: previous definition is here
#define NDEBUG 1
        ^
1 warning generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC  -Wall -g -O2  -c squid/dayhoff.c -o squid/dayhoff.o
In file included from squid/dayhoff.c:28:
In file included from squid/squid.h:32:
squid/../config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined]
#define NDEBUG /**/
        ^
:1:9: note: previous definition is here
#define NDEBUG 1
        ^
1 warning generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC  -Wall -g -O2  -c squid/eps.c -o squid/eps.o
In file included from squid/eps.c:23:
In file included from squid/squid.h:32:
squid/../config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined]
#define NDEBUG /**/
        ^
:1:9: note: previous definition is here
#define NDEBUG 1
        ^
1 warning generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC  -Wall -g -O2  -c squid/file.c -o squid/file.o
In file included from squid/file.c:28:
In file included from squid/squid.h:32:
squid/../config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined]
#define NDEBUG /**/
        ^
:1:9: note: previous definition is here
#define NDEBUG 1
        ^
1 warning generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC  -Wall -g -O2  -c squid/getopt.c -o squid/getopt.o
In file included from squid/getopt.c:17:
In file included from squid/squid.h:32:
squid/../config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined]
#define NDEBUG /**/
        ^
:1:9: note: previous definition is here
#define NDEBUG 1
        ^
1 warning generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC  -Wall -g -O2  -c squid/gki.c -o squid/gki.o
In file included from squid/gki.c:82:
In file included from squid/squid.h:32:
squid/../config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined]
#define NDEBUG /**/
        ^
:1:9: note: previous definition is here
#define NDEBUG 1
        ^
1 warning generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC  -Wall -g -O2  -c squid/gsi.c -o squid/gsi.o
In file included from squid/gsi.c:35:
In file included from squid/squid.h:32:
squid/../config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined]
#define NDEBUG /**/
        ^
:1:9: note: previous definition is here
#define NDEBUG 1
        ^
1 warning generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC  -Wall -g -O2  -c squid/gsi64.c -o squid/gsi64.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC  -Wall -g -O2  -c squid/hsregex.c -o squid/hsregex.o
In file included from squid/hsregex.c:33:
In file included from squid/squid.h:32:
squid/../config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined]
#define NDEBUG /**/
        ^
:1:9: note: previous definition is here
#define NDEBUG 1
        ^
1 warning generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC  -Wall -g -O2  -c squid/iupac.c -o squid/iupac.o
In file included from squid/iupac.c:17:
In file included from squid/squid.h:32:
squid/../config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined]
#define NDEBUG /**/
        ^
:1:9: note: previous definition is here
#define NDEBUG 1
        ^
1 warning generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC  -Wall -g -O2  -c squid/msa.c -o squid/msa.o
In file included from squid/msa.c:22:
In file included from squid/squid.h:32:
squid/../config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined]
#define NDEBUG /**/
        ^
:1:9: note: previous definition is here
#define NDEBUG 1
        ^
1 warning generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC  -Wall -g -O2  -c squid/msf.c -o squid/msf.o
In file included from squid/msf.c:25:
In file included from squid/squid.h:32:
squid/../config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined]
#define NDEBUG /**/
        ^
:1:9: note: previous definition is here
#define NDEBUG 1
        ^
1 warning generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC  -Wall -g -O2  -c squid/phylip.c -o squid/phylip.o
In file included from squid/phylip.c:23:
In file included from squid/squid.h:32:
squid/../config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined]
#define NDEBUG /**/
        ^
:1:9: note: previous definition is here
#define NDEBUG 1
        ^
1 warning generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC  -Wall -g -O2  -c squid/revcomp.c -o squid/revcomp.o
In file included from squid/revcomp.c:19:
In file included from squid/squid.h:32:
squid/../config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined]
#define NDEBUG /**/
        ^
:1:9: note: previous definition is here
#define NDEBUG 1
        ^
1 warning generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC  -Wall -g -O2  -c squid/rk.c -o squid/rk.o
In file included from squid/rk.c:26:
In file included from squid/squid.h:32:
squid/../config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined]
#define NDEBUG /**/
        ^
:1:9: note: previous definition is here
#define NDEBUG 1
        ^
1 warning generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC  -Wall -g -O2  -c squid/selex.c -o squid/selex.o
In file included from squid/selex.c:43:
In file included from squid/squid.h:32:
squid/../config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined]
#define NDEBUG /**/
        ^
:1:9: note: previous definition is here
#define NDEBUG 1
        ^
1 warning generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC  -Wall -g -O2  -c squid/seqencode.c -o squid/seqencode.o
In file included from squid/seqencode.c:18:
In file included from squid/squid.h:32:
squid/../config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined]
#define NDEBUG /**/
        ^
:1:9: note: previous definition is here
#define NDEBUG 1
        ^
1 warning generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC  -Wall -g -O2  -c squid/shuffle.c -o squid/shuffle.o
In file included from squid/shuffle.c:42:
In file included from squid/squid.h:32:
squid/../config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined]
#define NDEBUG /**/
        ^
:1:9: note: previous definition is here
#define NDEBUG 1
        ^
1 warning generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC  -Wall -g -O2  -c squid/sqerror.c -o squid/sqerror.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC  -Wall -g -O2  -c squid/sqio.c -o squid/sqio.o
In file included from squid/sqio.c:57:
In file included from squid/squid.h:32:
squid/../config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined]
#define NDEBUG /**/
        ^
:1:9: note: previous definition is here
#define NDEBUG 1
        ^
1 warning generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC  -Wall -g -O2  -c squid/squidcore.c -o squid/squidcore.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC  -Wall -g -O2  -c squid/sre_ctype.c -o squid/sre_ctype.o
In file included from squid/sre_ctype.c:19:
In file included from squid/squid.h:32:
squid/../config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined]
#define NDEBUG /**/
        ^
:1:9: note: previous definition is here
#define NDEBUG 1
        ^
1 warning generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC  -Wall -g -O2  -c squid/sre_math.c -o squid/sre_math.o
In file included from squid/sre_math.c:19:
In file included from squid/squid.h:32:
squid/../config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined]
#define NDEBUG /**/
        ^
:1:9: note: previous definition is here
#define NDEBUG 1
        ^
1 warning generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC  -Wall -g -O2  -c squid/sre_random.c -o squid/sre_random.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC  -Wall -g -O2  -c squid/sre_string.c -o squid/sre_string.o
In file included from squid/sre_string.c:23:
In file included from squid/squid.h:32:
squid/../config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined]
#define NDEBUG /**/
        ^
:1:9: note: previous definition is here
#define NDEBUG 1
        ^
1 warning generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC  -Wall -g -O2  -c squid/ssi.c -o squid/ssi.o
In file included from squid/ssi.c:16:
In file included from squid/squid.h:32:
squid/../config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined]
#define NDEBUG /**/
        ^
:1:9: note: previous definition is here
#define NDEBUG 1
        ^
1 warning generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC  -Wall -g -O2  -c squid/stack.c -o squid/stack.o
In file included from squid/stack.c:18:
In file included from squid/squid.h:32:
squid/../config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined]
#define NDEBUG /**/
        ^
:1:9: note: previous definition is here
#define NDEBUG 1
        ^
1 warning generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC  -Wall -g -O2  -c squid/stockholm.c -o squid/stockholm.o
In file included from squid/stockholm.c:31:
In file included from squid/squid.h:32:
squid/../config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined]
#define NDEBUG /**/
        ^
:1:9: note: previous definition is here
#define NDEBUG 1
        ^
1 warning generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC  -Wall -g -O2  -c squid/stopwatch.c -o squid/stopwatch.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC  -Wall -g -O2  -c squid/translate.c -o squid/translate.o
In file included from squid/translate.c:19:
In file included from squid/squid.h:32:
squid/../config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined]
#define NDEBUG /**/
        ^
:1:9: note: previous definition is here
#define NDEBUG 1
        ^
1 warning generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC  -Wall -g -O2  -c squid/types.c -o squid/types.o
In file included from squid/types.c:20:
In file included from squid/squid.h:32:
squid/../config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined]
#define NDEBUG /**/
        ^
:1:9: note: previous definition is here
#define NDEBUG 1
        ^
1 warning generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC  -Wall -g -O2  -c squid/vectorops.c -o squid/vectorops.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC  -Wall -g -O2  -c squid/weight.c -o squid/weight.o
In file included from squid/weight.c:19:
In file included from squid/squid.h:32:
squid/../config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined]
#define NDEBUG /**/
        ^
:1:9: note: previous definition is here
#define NDEBUG 1
        ^
1 warning generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -DMATH_H_CLIB -std=c++98 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC  -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
In file included from hhalign/hhalign.cpp:77:
hhalign/hhalignment-C.h:1908:43: warning: add explicit braces to avoid dangling else [-Wdangling-else]
                  if(in[k] && X[k][i]0) wi[k]=wg[k]; else wi[k]=0.0;
                                                                    ^
hhalign/hhalignment-C.h:2347:76: warning: add explicit braces to avoid dangling else [-Wdangling-else]
                                    if(in[k] && X[k][i]==GAP) wi[k]=wg[k]; else wi[k]=0.0;
                                                                           ^
In file included from hhalign/hhalign.cpp: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]=='.')
      ~~^~~ ~~
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 */
                ^
15 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -DMATH_H_CLIB -std=c++98 -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC  -Wall -g -O2  -c RClustalOmega.cpp -o RClustalOmega.o
In file included from RClustalOmega.cpp:27:
./config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined]
#define NDEBUG /**/
        ^
:1:9: note: previous definition is here
#define NDEBUG 1
        ^
1 warning generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC  -Wall -g -O2  -c mymain.c -o mymain.o
In file included from mymain.c:22:
./config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined]
#define NDEBUG /**/
        ^
:1:9: note: previous definition is here
#define NDEBUG 1
        ^
1 warning generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -fPIC  -Wall -g -O2  -c clustal-omega.c -o clustal-omega.o
In file included from clustal-omega.c:22:
./config.h:132:9: warning: 'NDEBUG' macro redefined [-Wmacro-redefined]
#define NDEBUG /**/
        ^
:1:9: note: previous definition is here
#define NDEBUG 1
        ^
clustal-omega.c:134:58: warning: implicit conversion from 'double' to 'int' changes value from 0.01 to 0 [-Wliteral-conversion]
static const int ITERATION_SCORE_IMPROVEMENT_THRESHOLD = 0.01;
                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   ^~~~
clustal-omega.c:134:18: warning: unused variable 'ITERATION_SCORE_IMPROVEMENT_THRESHOLD' [-Wunused-const-variable]
static const int ITERATION_SCORE_IMPROVEMENT_THRESHOLD = 0.01;
                 ^
3 warnings generated.
clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/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++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/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 /Library/Frameworks/R.framework/Versions/3.6/Resources/library/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)
name	user	system	elapsed
MsaMetaData-class	1.172	0.189	1.368
MsaMultipleAlignmentClasses	0.361	0.021	0.382
msa-package	0.261	0.005	0.270
msa	0.734	0.063	0.799
msaCheckNames	0.064	0.002	0.067
msaClustalOmega	0.608	0.125	0.738
msaClustalW	0.451	0.004	0.456
msaConsensusSequence-methods	0.183	0.003	0.187
msaConservationScore-methods	1.576	0.069	1.649
msaConvert	0.264	0.034	0.299
msaMuscle	0.634	0.013	0.647
msaPrettyPrint	6.193	0.240	6.473
CHECK report for msa on celaya2

Summary

Command output

Installation output

Tests output

Example timings
