BioC 3.1: CHECK report for msa on petty

Package: msa

Version: 1.0.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings msa_1.0.2.tar.gz

StartedAt: 2015-10-09 00:30:11 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 00:51:12 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 1261.1 seconds

RetCode: 0

Status:  OK

CheckDir: msa.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings msa_1.0.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/msa.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘msa/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘msa’ version ‘1.0.2’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘msa’ can be installed ... [7m/18m] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [20s/20s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
msaPrettyPrint 8.366  0.184    8.87
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK

* installing *source* package ‘msa’ ...
** libs
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"  -I"./gc-7.2/include" -I"./Muscle/" -I"./ClustalW/src" -I"./ClustalOmega/src" `Rscript -e "Rcpp:::CxxFlags()"` -fPIC  -mtune=core2 -g -O2 -Wall  -c R_init_msa.cpp -o R_init_msa.o
./Muscle/intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
make --file=msaMakefile --directory=gc-7.2
./configure --enable-cplusplus --enable-threads=pthreads --enable-shared --with-pic
checking build system type... x86_64-apple-darwin10.8.0
checking host system type... x86_64-apple-darwin10.8.0
checking target system type... x86_64-apple-darwin10.8.0
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... /usr/llvm-gcc-4.2/libexec/gcc/i686-apple-darwin10/4.2.1/ld
checking if the linker (/usr/llvm-gcc-4.2/libexec/gcc/i686-apple-darwin10/4.2.1/ld) is GNU ld... no
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm
checking the name lister (/usr/bin/nm) 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-darwin10.8.0 file names to x86_64-apple-darwin10.8.0 format... func_convert_file_noop
checking how to convert x86_64-apple-darwin10.8.0 file names to toolchain format... func_convert_file_noop
checking for /usr/llvm-gcc-4.2/libexec/gcc/i686-apple-darwin10/4.2.1/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 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... no
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 (/usr/llvm-gcc-4.2/libexec/gcc/i686-apple-darwin10/4.2.1/ld) supports shared libraries... yes
checking dynamic linker characteristics... darwin10.8.0 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++... /usr/llvm-gcc-4.2/libexec/gcc/i686-apple-darwin10/4.2.1/ld
checking if the linker (/usr/llvm-gcc-4.2/libexec/gcc/i686-apple-darwin10/4.2.1/ld) is GNU ld... no
checking whether the g++ linker (/usr/llvm-gcc-4.2/libexec/gcc/i686-apple-darwin10/4.2.1/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 (/usr/llvm-gcc-4.2/libexec/gcc/i686-apple-darwin10/4.2.1/ld) supports shared libraries... yes
checking dynamic linker characteristics... darwin10.8.0 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/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-3.1-bioc/meat/msa.Rcheck/00_pkg_src/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=/Library/Frameworks/GTK+.framework/Resources/lib/pkgconfig:/usr/lib/pkgconfig:/usr/local/lib/pkgconfig:/usr/X11/lib/pkgconfig:/usr/local/ggobi/lib/pkgconfig' --cache-file=/dev/null --srcdir=.
checking build system type... x86_64-apple-darwin10.8.0
checking host system type... x86_64-apple-darwin10.8.0
checking target system type... x86_64-apple-darwin10.8.0
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 $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT dyn_load.lo -MD -MP -MF .deps/dyn_load.Tpo -c dyn_load.c  -fno-common -DPIC -o .libs/dyn_load.o
dyn_load.c: In function ‘GC_init_dyld’:
dyn_load.c:1389: warning: passing argument 1 of ‘_dyld_register_func_for_add_image’ from incompatible pointer type
dyn_load.c:1390: warning: passing argument 1 of ‘_dyld_register_func_for_remove_image’ from incompatible pointer type
dyn_load.c:1413: warning: ‘_dyld_bind_fully_image_containing_address’ is deprecated (declared at /usr/include/mach-o/dyld.h:241)
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT dyn_load.lo -MD -MP -MF .deps/dyn_load.Tpo -c dyn_load.c  -fno-common -DPIC -o dyn_load.o >/dev/null 2>&1
depbase=`echo finalize.lo | sed 's|[^/]*$|.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 $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT typd_mlc.lo -MD -MP -MF .deps/typd_mlc.Tpo -c typd_mlc.c  -fno-common -DPIC -o .libs/typd_mlc.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -fno-strict-aliasing -MT typd_mlc.lo -MD -MP -MF .deps/typd_mlc.Tpo -c typd_mlc.c  -fno-common -DPIC -o typd_mlc.o >/dev/null 2>&1
depbase=`echo backgraph.lo | sed 's|[^/]*$|.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
/usr/bin/ranlib: file: .libs/libgc.a(checksums.o) has no symbols
/usr/bin/ranlib: file: .libs/libgc.a(gc_dlopen.o) has no symbols
/usr/bin/ranlib: file: .libs/libgc.a(pcr_interface.o) has no symbols
/usr/bin/ranlib: file: .libs/libgc.a(real_malloc.o) has no symbols
/usr/bin/ranlib: file: .libs/libgc.a(specific.o) has no symbols
/usr/bin/ranlib: file: .libs/libgc.a(backgraph.o) has no symbols
/usr/bin/ranlib: file: .libs/libgc.a(pthread_stop_world.o) has no symbols
libtool: link: ranlib .libs/libgc.a
ranlib: file: .libs/libgc.a(checksums.o) has no symbols
ranlib: file: .libs/libgc.a(gc_dlopen.o) has no symbols
ranlib: file: .libs/libgc.a(pcr_interface.o) has no symbols
ranlib: file: .libs/libgc.a(real_malloc.o) has no symbols
ranlib: file: .libs/libgc.a(specific.o) has no symbols
ranlib: file: .libs/libgc.a(backgraph.o) has no symbols
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 $depbase.Plo
libtool: compile:  g++ -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -MT gc_cpp.lo -MD -MP -MF .deps/gc_cpp.Tpo -c gc_cpp.cc  -fno-common -DPIC -o .libs/gc_cpp.o
libtool: compile:  g++ -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -g -O2 -MT gc_cpp.lo -MD -MP -MF .deps/gc_cpp.Tpo -c gc_cpp.cc  -fno-common -DPIC -o gc_cpp.o >/dev/null 2>&1
/bin/sh ./libtool  --tag=CXX   --mode=link g++ -fexceptions -g -O2 -version-info 1:3:0 -no-undefined  -o libgccpp.la -rpath /usr/local/lib gc_cpp.lo ./libgc.la 
libtool: link: g++ -dynamiclib  -o .libs/libgccpp.1.dylib  .libs/gc_cpp.o   ./.libs/libgc.dylib -lpthread  -g -O2   -install_name  /usr/local/lib/libgccpp.1.dylib -compatibility_version 2 -current_version 2.3 -Wl,-single_module
libtool: link: (cd ".libs" && rm -f "libgccpp.dylib" && ln -s "libgccpp.1.dylib" "libgccpp.dylib")
libtool: link: ar cru .libs/libgccpp.a  gc_cpp.o
libtool: link: ranlib .libs/libgccpp.a
libtool: link: ( cd ".libs" && rm -f "libgccpp.la" && ln -s "../libgccpp.la" "libgccpp.la" )
depbase=`echo cord/cordbscs.lo | sed 's|[^/]*$|.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" `Rscript -e "Rcpp:::CxxFlags()"`"
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
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c aligngivenpath.cpp -o aligngivenpath.o
aligngivenpath.cpp: In function ‘void AppendTplInserts(const MSA&, unsigned int&, unsigned int, const MSA&, unsigned int&, unsigned int, unsigned int, unsigned int, MSA&, unsigned int&)’:
aligngivenpath.cpp:186: warning: unused variable ‘uLengthA’
aligngivenpath.cpp:187: warning: unused variable ‘uLengthB’
aligngivenpath.cpp: In function ‘void AlignTwoMSAsGivenPath(const PWPath&, const MSA&, const MSA&, MSA&)’:
aligngivenpath.cpp:335: warning: unused variable ‘uColA’
aligngivenpath.cpp:336: warning: unused variable ‘uColB’
aligngivenpath.cpp:346: warning: unused variable ‘uColA’
aligngivenpath.cpp:354: warning: unused variable ‘uColB’
intmath.h: At global scope:
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c aligngivenpathsw.cpp -o aligngivenpathsw.o
aligngivenpathsw.cpp: In function ‘void AppendUnalignedTerminals(const MSA&, unsigned int&, unsigned int, const MSA&, unsigned int&, unsigned int, unsigned int, unsigned int, MSA&, unsigned int&)’:
aligngivenpathsw.cpp:58: warning: unused variable ‘uLengthA’
aligngivenpathsw.cpp:59: warning: unused variable ‘uLengthB’
aligngivenpathsw.cpp: In function ‘void AlignTwoMSAsGivenPathSW(const PWPath&, const MSA&, const MSA&, MSA&)’:
aligngivenpathsw.cpp:204: warning: unused variable ‘uColA’
aligngivenpathsw.cpp:205: warning: unused variable ‘uColB’
aligngivenpathsw.cpp:215: warning: unused variable ‘uColA’
aligngivenpathsw.cpp:223: warning: unused variable ‘uColB’
intmath.h: At global scope:
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c aligntwomsas.cpp -o aligntwomsas.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c aligntwoprofs.cpp -o aligntwoprofs.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c aln.cpp -o aln.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c alpha.cpp -o alpha.o
alpha.cpp: In function ‘unsigned int GetAlphaSize(ALPHA)’:
alpha.cpp:84: warning: enumeration value ‘ALPHA_Undefined’ not handled in switch
intmath.h: At global scope:
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c anchors.cpp -o anchors.o
anchors.cpp: In function ‘void MergeBestCols(const SCORE*, const unsigned int*, unsigned int, unsigned int, unsigned int*, unsigned int*)’:
anchors.cpp:162: warning: unused variable ‘uWindowCenter’
intmath.h: At global scope:
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
anchors.cpp:54: warning: ‘void FindBestColsGrade(const SCORE*, unsigned int, double, unsigned int*, unsigned int*)’ defined but not used
anchors.cpp:106: warning: ‘void ListBestCols(const MSA&, const SCORE*, const SCORE*, unsigned int*, unsigned int)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c bittraceback.cpp -o bittraceback.o
bittraceback.cpp: In function ‘void BitTraceBack(char**, unsigned int, unsigned int, char, PWPath&)’:
bittraceback.cpp:146: warning: unused variable ‘Bits’
intmath.h: At global scope:
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
bittraceback.cpp:15: warning: ‘const char* BitsToStr(char)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c blosum62.cpp -o blosum62.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c blosumla.cpp -o blosumla.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
blosumla.cpp:7: warning: ‘Blosum62LA’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c clust.cpp -o clust.o
clust.cpp: In member function ‘void Clust::ChooseJoin(unsigned int*, unsigned int*, float*, float*)’:
clust.cpp:167: warning: enumeration value ‘JOIN_Undefined’ not handled in switch
clust.cpp: In member function ‘void Clust::ChooseJoinNearestNeighbor(unsigned int*, unsigned int*, float*, float*)’:
clust.cpp:184: warning: unused variable ‘uClusterCount’
clust.cpp: In member function ‘void Clust::ChooseJoinNeighborJoining(unsigned int*, unsigned int*, float*, float*)’:
clust.cpp:204: warning: unused variable ‘uClusterCount’
clust.cpp: In member function ‘float Clust::ComputeDist(unsigned int, unsigned int)’:
clust.cpp:295: warning: enumeration value ‘LINKAGE_Undefined’ not handled in switch
clust.cpp: In member function ‘float Clust::ComputeDistMAFFT(unsigned int, unsigned int)’:
clust.cpp:360: warning: unused variable ‘dDistLR’
clust.cpp: In member function ‘float Clust::ComputeMetric(unsigned int, unsigned int) const’:
clust.cpp:611: warning: enumeration value ‘JOIN_Undefined’ not handled in switch
intmath.h: At global scope:
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c cluster.cpp -o cluster.o
cluster.cpp: In member function ‘void ClusterTree::Create(const DistFunc&)’:
cluster.cpp:267: warning: unused variable ‘dMaxDist’
intmath.h: At global scope:
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c clwwt.cpp -o clwwt.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c color.cpp -o color.o
color.cpp:34: warning: missing braces around initializer for ‘int [23]’
color.cpp:34: warning: missing braces around initializer for ‘int [23]’
color.cpp:34: warning: missing braces around initializer for ‘int [23]’
color.cpp:34: warning: missing braces around initializer for ‘int [23]’
color.cpp:34: warning: missing braces around initializer for ‘int [23]’
color.cpp:34: warning: missing braces around initializer for ‘int [23]’
color.cpp:34: warning: missing braces around initializer for ‘int [23]’
color.cpp:34: warning: missing braces around initializer for ‘int [23]’
color.cpp:34: warning: missing braces around initializer for ‘int [23]’
color.cpp:34: warning: missing braces around initializer for ‘int [23]’
color.cpp:34: warning: missing braces around initializer for ‘int [23]’
color.cpp:34: warning: missing braces around initializer for ‘int [23]’
color.cpp:34: warning: missing braces around initializer for ‘int [23]’
color.cpp:34: warning: missing braces around initializer for ‘int [23]’
color.cpp:34: warning: missing braces around initializer for ‘int [23]’
color.cpp:34: warning: missing braces around initializer for ‘int [23]’
color.cpp:34: warning: missing braces around initializer for ‘int [23]’
color.cpp:34: warning: missing braces around initializer for ‘int [23]’
color.cpp:34: warning: missing braces around initializer for ‘int [23]’
color.cpp:34: warning: missing braces around initializer for ‘int [23]’
color.cpp:34: warning: missing braces around initializer for ‘int [23]’
color.cpp:34: warning: missing braces around initializer for ‘int [23]’
color.cpp:34: warning: missing braces around initializer for ‘int [23]’
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
color.cpp:72: warning: ‘int BlosumScore(char, char)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c cons.cpp -o cons.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c diaglist.cpp -o diaglist.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c diffobjscore.cpp -o diffobjscore.o
diffobjscore.cpp: In function ‘SCORE ScoreLetters(const MSA&, const unsigned int*, unsigned int)’:
diffobjscore.cpp:76: warning: unused variable ‘uSeqCount’
diffobjscore.cpp:77: warning: unused variable ‘uColCount’
intmath.h: At global scope:
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c diffpaths.cpp -o diffpaths.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c difftrees.cpp -o difftrees.o
difftrees.cpp: In function ‘void DiffTrees(const Tree&, const Tree&, Tree&, unsigned int*)’:
difftrees.cpp:161: warning: unused variable ‘uLeafCount2’
intmath.h: At global scope:
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c difftreese.cpp -o difftreese.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c distcalc.cpp -o distcalc.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c distfunc.cpp -o distfunc.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c distpwkimura.cpp -o distpwkimura.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c domuscle.cpp -o domuscle.o
domuscle.cpp: In function ‘void DoMuscle(MuscleInput*, MuscleOutput*)’:
domuscle.cpp:180: warning: unused variable ‘PNlength’
intmath.h: At global scope:
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c dosp.cpp -o dosp.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c dpreglist.cpp -o dpreglist.o
dpreglist.cpp: In function ‘void DiagListToDPRegionList(const DiagList&, DPRegionList&, unsigned int, unsigned int)’:
dpreglist.cpp:82: warning: unused variable ‘uDiagLengthMinusCaps’
intmath.h: At global scope:
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c drawtree.cpp -o drawtree.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c edgelist.cpp -o edgelist.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c enumopts.cpp -o enumopts.o
In file included from enumopts.cpp:8:
enums.h:15: warning: missing braces around initializer for ‘EnumOpt’
enums.h:15: warning: missing braces around initializer for ‘EnumOpt’
enums.h:15: warning: missing braces around initializer for ‘EnumOpt’
enums.h:15: warning: missing braces around initializer for ‘EnumOpt’
enums.h:22: warning: missing braces around initializer for ‘EnumOpt’
enums.h:22: warning: missing braces around initializer for ‘EnumOpt’
enums.h:22: warning: missing braces around initializer for ‘EnumOpt’
enums.h:22: warning: missing braces around initializer for ‘EnumOpt’
enums.h:22: warning: missing braces around initializer for ‘EnumOpt’
enums.h:28: warning: missing braces around initializer for ‘EnumOpt’
enums.h:28: warning: missing braces around initializer for ‘EnumOpt’
enums.h:28: warning: missing braces around initializer for ‘EnumOpt’
enums.h:28: warning: missing braces around initializer for ‘EnumOpt’
enums.h:36: warning: missing braces around initializer for ‘EnumOpt’
enums.h:36: warning: missing braces around initializer for ‘EnumOpt’
enums.h:36: warning: missing braces around initializer for ‘EnumOpt’
enums.h:36: warning: missing braces around initializer for ‘EnumOpt’
enums.h:36: warning: missing braces around initializer for ‘EnumOpt’
enums.h:36: warning: missing braces around initializer for ‘EnumOpt’
enums.h:41: warning: missing braces around initializer for ‘EnumOpt’
enums.h:41: warning: missing braces around initializer for ‘EnumOpt’
enums.h:41: warning: missing braces around initializer for ‘EnumOpt’
enums.h:49: warning: missing braces around initializer for ‘EnumOpt’
enums.h:49: warning: missing braces around initializer for ‘EnumOpt’
enums.h:49: warning: missing braces around initializer for ‘EnumOpt’
enums.h:49: warning: missing braces around initializer for ‘EnumOpt’
enums.h:49: warning: missing braces around initializer for ‘EnumOpt’
enums.h:49: warning: missing braces around initializer for ‘EnumOpt’
enums.h:63: warning: missing braces around initializer for ‘EnumOpt’
enums.h:63: warning: missing braces around initializer for ‘EnumOpt’
enums.h:63: warning: missing braces around initializer for ‘EnumOpt’
enums.h:63: warning: missing braces around initializer for ‘EnumOpt’
enums.h:63: warning: missing braces around initializer for ‘EnumOpt’
enums.h:63: warning: missing braces around initializer for ‘EnumOpt’
enums.h:63: warning: missing braces around initializer for ‘EnumOpt’
enums.h:63: warning: missing braces around initializer for ‘EnumOpt’
enums.h:63: warning: missing braces around initializer for ‘EnumOpt’
enums.h:63: warning: missing braces around initializer for ‘EnumOpt’
enums.h:63: warning: missing braces around initializer for ‘EnumOpt’
enums.h:63: warning: missing braces around initializer for ‘EnumOpt’
enums.h:70: warning: missing braces around initializer for ‘EnumOpt’
enums.h:70: warning: missing braces around initializer for ‘EnumOpt’
enums.h:70: warning: missing braces around initializer for ‘EnumOpt’
enums.h:70: warning: missing braces around initializer for ‘EnumOpt’
enums.h:70: warning: missing braces around initializer for ‘EnumOpt’
enums.h:79: warning: missing braces around initializer for ‘EnumOpt’
enums.h:79: warning: missing braces around initializer for ‘EnumOpt’
enums.h:79: warning: missing braces around initializer for ‘EnumOpt’
enums.h:79: warning: missing braces around initializer for ‘EnumOpt’
enums.h:79: warning: missing braces around initializer for ‘EnumOpt’
enums.h:79: warning: missing braces around initializer for ‘EnumOpt’
enums.h:79: warning: missing braces around initializer for ‘EnumOpt’
enums.h:88: warning: missing braces around initializer for ‘EnumOpt’
enums.h:88: warning: missing braces around initializer for ‘EnumOpt’
enums.h:88: warning: missing braces around initializer for ‘EnumOpt’
enums.h:88: warning: missing braces around initializer for ‘EnumOpt’
enums.h:88: warning: missing braces around initializer for ‘EnumOpt’
enums.h:88: warning: missing braces around initializer for ‘EnumOpt’
enums.h:88: warning: missing braces around initializer for ‘EnumOpt’
enums.h:94: warning: missing braces around initializer for ‘EnumOpt’
enums.h:94: warning: missing braces around initializer for ‘EnumOpt’
enums.h:94: warning: missing braces around initializer for ‘EnumOpt’
enums.h:94: warning: missing braces around initializer for ‘EnumOpt’
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c enumtostr.cpp -o enumtostr.o
In file included from enumtostr.cpp:16:
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c estring.cpp -o estring.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
estring.cpp:464: warning: ‘bool CanMultiplyEstrings(const short int*, const short int*)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c fasta.cpp -o fasta.o
fasta.cpp: In member function ‘void MSA::FromFASTAFile(TextFile&)’:
fasta.cpp:15: warning: unused variable ‘uSeqCount’
fasta.cpp:16: warning: unused variable ‘uColCount’
intmath.h: At global scope:
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c fasta2.cpp -o fasta2.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c fastclust.cpp -o fastclust.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c fastdist.cpp -o fastdist.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c fastdistjones.cpp -o fastdistjones.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c fastdistkbit.cpp -o fastdistkbit.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c fastdistkmer.cpp -o fastdistkmer.o
fastdistkmer.cpp: In function ‘void FastDistKmer(const SeqVect&, DistFunc&)’:
fastdistkmer.cpp:235: warning: unused variable ‘KD’
intmath.h: At global scope:
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c fastdistmafft.cpp -o fastdistmafft.o
fastdistmafft.cpp: In function ‘void DistKmer6_6(const SeqVect&, DistFunc&)’:
fastdistmafft.cpp:239: warning: unused variable ‘pName1’
intmath.h: At global scope:
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
fastdistmafft.cpp:104: warning: ‘void ListCount(const unsigned char*)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c fastdistnuc.cpp -o fastdistnuc.o
fastdistnuc.cpp: In function ‘void DistKmer4_6(const SeqVect&, DistFunc&)’:
fastdistnuc.cpp:223: warning: unused variable ‘pName1’
intmath.h: At global scope:
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
fastdistnuc.cpp:33: warning: ‘uResidueGroupCount’ defined but not used
fastdistnuc.cpp:85: warning: ‘void ListCount(const unsigned char*)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c fastscorepath2.cpp -o fastscorepath2.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c finddiags.cpp -o finddiags.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
finddiags.cpp:11: warning: ‘char* TupleToStr(int)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c finddiagsn.cpp -o finddiagsn.o
finddiagsn.cpp: In function ‘char* TupleToStr(int)’:
finddiagsn.cpp:16: warning: comparison between signed and unsigned integer expressions
intmath.h: At global scope:
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
finddiagsn.cpp:12: warning: ‘char* TupleToStr(int)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c glbalign.cpp -o glbalign.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c glbalign352.cpp -o glbalign352.o
In file included from glbalign352.cpp:6:
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c glbaligndiag.cpp -o glbaligndiag.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c glbalignle.cpp -o glbalignle.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c glbalignsimple.cpp -o glbalignsimple.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
glbalignsimple.cpp:29: warning: ‘void ListTB(const char*, const ProfPos*, const ProfPos*, unsigned int, unsigned int)’ defined but not used
glbalignsimple.cpp:53: warning: ‘void ListDP(const SCORE*, const ProfPos*, const ProfPos*, unsigned int, unsigned int)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c glbalignsp.cpp -o glbalignsp.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c glbalignspn.cpp -o glbalignspn.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c glbalignss.cpp -o glbalignss.o
glbalignss.cpp: In function ‘SCORE GlobalAlignSS(const Seq&, const Seq&, PWPath&)’:
glbalignss.cpp:177: warning: unused variable ‘ptrRowA’
glbalignss.cpp:119: warning: unused variable ‘uPrefixCountA’
glbalignss.cpp:120: warning: unused variable ‘uPrefixCountB’
intmath.h: At global scope:
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
glbalignss.cpp:11: warning: ‘SCORE Subst(const Seq&, const Seq&, unsigned int, unsigned int)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c glbalndimer.cpp -o glbalndimer.o
glbalndimer.cpp: In function ‘SCORE ScoreProfPosDimer(const ProfPos&, const ProfPos&)’:
glbalndimer.cpp:123: warning: enumeration value ‘PPSCORE_Undefined’ not handled in switch
glbalndimer.cpp:123: warning: enumeration value ‘PPSCORE_SPN’ not handled in switch
intmath.h: At global scope:
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
glbalndimer.cpp:14: warning: ‘const char* LocalScoreToStr(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c globals.cpp -o globals.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c globalslinux.cpp -o globalslinux.o
In file included from globalslinux.cpp:1:
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c globalsosx.cpp -o globalsosx.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c globalsother.cpp -o globalsother.o
In file included from globalsother.cpp:1:
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c globalswin32.cpp -o globalswin32.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c gonnet.cpp -o gonnet.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
gonnet.cpp:137: warning: ‘Gonnet160’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c henikoffweight.cpp -o henikoffweight.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c henikoffweightpb.cpp -o henikoffweightpb.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c html.cpp -o html.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c hydro.cpp -o hydro.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c intmath.cpp -o intmath.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c local.cpp -o local.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c main.cpp -o main.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c makerootmsa.cpp -o makerootmsa.o
makerootmsa.cpp: In function ‘void PathSeq(const Seq&, const PWPath&, bool, Seq&)’:
makerootmsa.cpp:18: warning: unused variable ‘uSeqLength’
makerootmsa.cpp: In function ‘short int* MakeRootSeqE(const Seq&, const Tree&, unsigned int, const ProgNode*, Seq&, short int*, short int*)’:
makerootmsa.cpp:94: warning: unused variable ‘Path’
makerootmsa.cpp: In function ‘void MakeRootMSA(const SeqVect&, const Tree&, ProgNode*, MSA&)’:
makerootmsa.cpp:168: warning: unused variable ‘uTreeNodeCount’
intmath.h: At global scope:
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
makerootmsa.cpp:12: warning: ‘void PathSeq(const Seq&, const PWPath&, bool, Seq&)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c makerootmsab.cpp -o makerootmsab.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c maketree.cpp -o maketree.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c mhack.cpp -o mhack.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c mpam200.cpp -o mpam200.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c msa.cpp -o msa.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
msa.cpp:385: warning: ‘void FmtChar(char, unsigned int)’ defined but not used
msa.cpp:392: warning: ‘void FmtInt(unsigned int, unsigned int)’ defined but not used
msa.cpp:407: warning: ‘void FmtInt0(unsigned int, unsigned int)’ defined but not used
msa.cpp:419: warning: ‘void FmtPad(unsigned int)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c msa2.cpp -o msa2.o
msa2.cpp: In function ‘void SetMSAWeightsMuscle(MSA&)’:
msa2.cpp:357: warning: enumeration value ‘SEQWEIGHT_Undefined’ not handled in switch
msa2.cpp: In function ‘void MSAAppend(MSA&, const MSA&)’:
msa2.cpp:476: warning: unused variable ‘uColCountCat’
intmath.h: At global scope:
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c msadistkimura.cpp -o msadistkimura.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c msf.cpp -o msf.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
msf.cpp:24: warning: ‘const char* strfind(const char*, const char*)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c muscle.cpp -o muscle.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c muscleout.cpp -o muscleout.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c nucmx.cpp -o nucmx.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c nwdasimple.cpp -o nwdasimple.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c nwdasimple2.cpp -o nwdasimple2.o
In file included from nwdasimple2.cpp:3:
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c nwdasmall.cpp -o nwdasmall.o
In file included from nwdasmall.cpp:4:
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c nwrec.cpp -o nwrec.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c nwsmall.cpp -o nwsmall.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c objscore.cpp -o objscore.o
objscore.cpp: In function ‘SCORE ObjScore(const MSA&, const unsigned int*, unsigned int, const unsigned int*, unsigned int)’:
objscore.cpp:31: warning: enumeration value ‘OBJSCORE_Undefined’ not handled in switch
objscore.cpp:31: warning: enumeration value ‘OBJSCORE_SPM’ not handled in switch
intmath.h: At global scope:
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c objscore2.cpp -o objscore2.o
objscore2.cpp: In function ‘SCORE TermGapScore(bool)’:
objscore2.cpp:22: warning: enumeration value ‘TERMGAPS_Undefined’ not handled in switch
objscore2.cpp: In function ‘SCORE ScoreSeqPairLetters(const MSA&, unsigned int, const MSA&, unsigned int)’:
objscore2.cpp:62: warning: unused variable ‘scoreGaps’
objscore2.cpp:63: warning: unused variable ‘bGapping1’
objscore2.cpp:64: warning: unused variable ‘bGapping2’
objscore2.cpp: In function ‘SCORE ObjScoreDP(const MSA&, const MSA&, SCORE*)’:
objscore2.cpp:314: warning: unused variable ‘uColCount2’
objscore2.cpp: In function ‘SCORE ObjScoreXP(const MSA&, const MSA&)’:
objscore2.cpp:493: warning: unused variable ‘w’
intmath.h: At global scope:
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c objscoreda.cpp -o objscoreda.o
In file included from objscoreda.cpp:4:
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c onexception.cpp -o onexception.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c options.cpp -o options.o
options.cpp:84: warning: missing braces around initializer for ‘VALUE_OPT’
options.cpp:84: warning: missing braces around initializer for ‘VALUE_OPT’
options.cpp:84: warning: missing braces around initializer for ‘VALUE_OPT’
options.cpp:84: warning: missing braces around initializer for ‘VALUE_OPT’
options.cpp:84: warning: missing braces around initializer for ‘VALUE_OPT’
options.cpp:84: warning: missing braces around initializer for ‘VALUE_OPT’
options.cpp:84: warning: missing braces around initializer for ‘VALUE_OPT’
options.cpp:84: warning: missing braces around initializer for ‘VALUE_OPT’
options.cpp:84: warning: missing braces around initializer for ‘VALUE_OPT’
options.cpp:84: warning: missing braces around initializer for ‘VALUE_OPT’
options.cpp:84: warning: missing braces around initializer for ‘VALUE_OPT’
options.cpp:84: warning: missing braces around initializer for ‘VALUE_OPT’
options.cpp:84: warning: missing braces around initializer for ‘VALUE_OPT’
options.cpp:84: warning: missing braces around initializer for ‘VALUE_OPT’
options.cpp:84: warning: missing braces around initializer for ‘VALUE_OPT’
options.cpp:84: warning: missing braces around initializer for ‘VALUE_OPT’
options.cpp:84: warning: missing braces around initializer for ‘VALUE_OPT’
options.cpp:84: warning: missing braces around initializer for ‘VALUE_OPT’
options.cpp:84: warning: missing braces around initializer for ‘VALUE_OPT’
options.cpp:84: warning: missing braces around initializer for ‘VALUE_OPT’
options.cpp:84: warning: missing braces around initializer for ‘VALUE_OPT’
options.cpp:84: warning: missing braces around initializer for ‘VALUE_OPT’
options.cpp:84: warning: missing braces around initializer for ‘VALUE_OPT’
options.cpp:84: warning: missing braces around initializer for ‘VALUE_OPT’
options.cpp:84: warning: missing braces around initializer for ‘VALUE_OPT’
options.cpp:84: warning: missing braces around initializer for ‘VALUE_OPT’
options.cpp:84: warning: missing braces around initializer for ‘VALUE_OPT’
options.cpp:84: warning: missing braces around initializer for ‘VALUE_OPT’
options.cpp:84: warning: missing braces around initializer for ‘VALUE_OPT’
options.cpp:84: warning: missing braces around initializer for ‘VALUE_OPT’
options.cpp:84: warning: missing braces around initializer for ‘VALUE_OPT’
options.cpp:84: warning: missing braces around initializer for ‘VALUE_OPT’
options.cpp:84: warning: missing braces around initializer for ‘VALUE_OPT’
options.cpp:84: warning: missing braces around initializer for ‘VALUE_OPT’
options.cpp:84: warning: missing braces around initializer for ‘VALUE_OPT’
options.cpp:84: warning: missing braces around initializer for ‘VALUE_OPT’
options.cpp:84: warning: missing braces around initializer for ‘VALUE_OPT’
options.cpp:84: warning: missing braces around initializer for ‘VALUE_OPT’
options.cpp:84: warning: missing braces around initializer for ‘VALUE_OPT’
options.cpp:84: warning: missing braces around initializer for ‘VALUE_OPT’
options.cpp:84: warning: missing braces around initializer for ‘VALUE_OPT’
options.cpp:84: warning: missing braces around initializer for ‘VALUE_OPT’
options.cpp:84: warning: missing braces around initializer for ‘VALUE_OPT’
options.cpp:84: warning: missing braces around initializer for ‘VALUE_OPT’
options.cpp:84: warning: missing braces around initializer for ‘VALUE_OPT’
options.cpp:84: warning: missing braces around initializer for ‘VALUE_OPT’
options.cpp:84: warning: missing braces around initializer for ‘VALUE_OPT’
options.cpp:84: warning: missing braces around initializer for ‘VALUE_OPT’
options.cpp:84: warning: missing braces around initializer for ‘VALUE_OPT’
options.cpp:84: warning: missing braces around initializer for ‘VALUE_OPT’
options.cpp:84: warning: missing braces around initializer for ‘VALUE_OPT’
options.cpp:84: warning: missing braces around initializer for ‘VALUE_OPT’
options.cpp:84: warning: missing braces around initializer for ‘VALUE_OPT’
options.cpp:84: warning: missing braces around initializer for ‘VALUE_OPT’
options.cpp:84: warning: missing braces around initializer for ‘VALUE_OPT’
options.cpp:84: warning: missing braces around initializer for ‘VALUE_OPT’
options.cpp:84: warning: missing braces around initializer for ‘VALUE_OPT’
options.cpp:84: warning: missing braces around initializer for ‘VALUE_OPT’
options.cpp:84: warning: missing braces around initializer for ‘VALUE_OPT’
options.cpp:84: warning: missing braces around initializer for ‘VALUE_OPT’
options.cpp:84: warning: missing braces around initializer for ‘VALUE_OPT’
options.cpp:84: warning: missing braces around initializer for ‘VALUE_OPT’
options.cpp:84: warning: missing braces around initializer for ‘VALUE_OPT’
options.cpp:84: warning: missing braces around initializer for ‘VALUE_OPT’
options.cpp:84: warning: missing braces around initializer for ‘VALUE_OPT’
options.cpp:84: warning: missing braces around initializer for ‘VALUE_OPT’
options.cpp:124: warning: missing braces around initializer for ‘FLAG_OPT’
options.cpp:124: warning: missing braces around initializer for ‘FLAG_OPT’
options.cpp:124: warning: missing braces around initializer for ‘FLAG_OPT’
options.cpp:124: warning: missing braces around initializer for ‘FLAG_OPT’
options.cpp:124: warning: missing braces around initializer for ‘FLAG_OPT’
options.cpp:124: warning: missing braces around initializer for ‘FLAG_OPT’
options.cpp:124: warning: missing braces around initializer for ‘FLAG_OPT’
options.cpp:124: warning: missing braces around initializer for ‘FLAG_OPT’
options.cpp:124: warning: missing braces around initializer for ‘FLAG_OPT’
options.cpp:124: warning: missing braces around initializer for ‘FLAG_OPT’
options.cpp:124: warning: missing braces around initializer for ‘FLAG_OPT’
options.cpp:124: warning: missing braces around initializer for ‘FLAG_OPT’
options.cpp:124: warning: missing braces around initializer for ‘FLAG_OPT’
options.cpp:124: warning: missing braces around initializer for ‘FLAG_OPT’
options.cpp:124: warning: missing braces around initializer for ‘FLAG_OPT’
options.cpp:124: warning: missing braces around initializer for ‘FLAG_OPT’
options.cpp:124: warning: missing braces around initializer for ‘FLAG_OPT’
options.cpp:124: warning: missing braces around initializer for ‘FLAG_OPT’
options.cpp:124: warning: missing braces around initializer for ‘FLAG_OPT’
options.cpp:124: warning: missing braces around initializer for ‘FLAG_OPT’
options.cpp:124: warning: missing braces around initializer for ‘FLAG_OPT’
options.cpp:124: warning: missing braces around initializer for ‘FLAG_OPT’
options.cpp:124: warning: missing braces around initializer for ‘FLAG_OPT’
options.cpp:124: warning: missing braces around initializer for ‘FLAG_OPT’
options.cpp:124: warning: missing braces around initializer for ‘FLAG_OPT’
options.cpp:124: warning: missing braces around initializer for ‘FLAG_OPT’
options.cpp:124: warning: missing braces around initializer for ‘FLAG_OPT’
options.cpp:124: warning: missing braces around initializer for ‘FLAG_OPT’
options.cpp:124: warning: missing braces around initializer for ‘FLAG_OPT’
options.cpp:124: warning: missing braces around initializer for ‘FLAG_OPT’
options.cpp:124: warning: missing braces around initializer for ‘FLAG_OPT’
options.cpp:124: warning: missing braces around initializer for ‘FLAG_OPT’
options.cpp:124: warning: missing braces around initializer for ‘FLAG_OPT’
options.cpp:124: warning: missing braces around initializer for ‘FLAG_OPT’
options.cpp:124: warning: missing braces around initializer for ‘FLAG_OPT’
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c outweights.cpp -o outweights.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c pam200mafft.cpp -o pam200mafft.o
pam200mafft.cpp:32: warning: missing braces around initializer for ‘float [23]’
pam200mafft.cpp:32: warning: missing braces around initializer for ‘float [23]’
pam200mafft.cpp:32: warning: missing braces around initializer for ‘float [23]’
pam200mafft.cpp:32: warning: missing braces around initializer for ‘float [23]’
pam200mafft.cpp:32: warning: missing braces around initializer for ‘float [23]’
pam200mafft.cpp:32: warning: missing braces around initializer for ‘float [23]’
pam200mafft.cpp:32: warning: missing braces around initializer for ‘float [23]’
pam200mafft.cpp:32: warning: missing braces around initializer for ‘float [23]’
pam200mafft.cpp:32: warning: missing braces around initializer for ‘float [23]’
pam200mafft.cpp:32: warning: missing braces around initializer for ‘float [23]’
pam200mafft.cpp:32: warning: missing braces around initializer for ‘float [23]’
pam200mafft.cpp:32: warning: missing braces around initializer for ‘float [23]’
pam200mafft.cpp:32: warning: missing braces around initializer for ‘float [23]’
pam200mafft.cpp:32: warning: missing braces around initializer for ‘float [23]’
pam200mafft.cpp:32: warning: missing braces around initializer for ‘float [23]’
pam200mafft.cpp:32: warning: missing braces around initializer for ‘float [23]’
pam200mafft.cpp:32: warning: missing braces around initializer for ‘float [23]’
pam200mafft.cpp:32: warning: missing braces around initializer for ‘float [23]’
pam200mafft.cpp:32: warning: missing braces around initializer for ‘float [23]’
pam200mafft.cpp:32: warning: missing braces around initializer for ‘float [23]’
pam200mafft.cpp:32: warning: missing braces around initializer for ‘float [23]’
pam200mafft.cpp:32: warning: missing braces around initializer for ‘float [23]’
pam200mafft.cpp:32: warning: missing braces around initializer for ‘float [23]’
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
pam200mafft.cpp:6: warning: ‘PAM200’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c params.cpp -o params.o
params.cpp: In function ‘void SetPPScore(bool)’:
params.cpp:441: warning: enumeration value ‘PPSCORE_Undefined’ not handled in switch
intmath.h: At global scope:
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c phy.cpp -o phy.o
phy.cpp: In member function ‘void Tree::RootUnrootedTree(ROOT)’:
phy.cpp:665: warning: unused variable ‘dEdgeLength’
intmath.h: At global scope:
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c phy2.cpp -o phy2.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c phy3.cpp -o phy3.o
phy3.cpp: In function ‘void CalcInfo(const Tree&, unsigned int, unsigned int, EdgeInfo**)’:
phy3.cpp:125: warning: unused variable ‘dThisDist’
phy3.cpp: In function ‘void FindRoot(const Tree&, unsigned int*, unsigned int*, double*, double*, ROOT)’:
phy3.cpp:167: warning: unused variable ‘uLeafCount’
phy3.cpp:190: warning: unused variable ‘dAllMaxDist’
phy3.cpp:191: warning: unused variable ‘uMaxFrom’
phy3.cpp:192: warning: unused variable ‘uMaxTo’
intmath.h: At global scope:
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
phy3.cpp:45: warning: ‘void ListEIs(EdgeInfo**, unsigned int)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c phy4.cpp -o phy4.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c phyfromclust.cpp -o phyfromclust.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c phyfromfile.cpp -o phyfromfile.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c physeq.cpp -o physeq.o
physeq.cpp: In member function ‘void MSA::ToPhySequentialFile(TextFile&) const’:
physeq.cpp:60: warning: comparison between signed and unsigned integer expressions
physeq.cpp:71: warning: comparison between signed and unsigned integer expressions
physeq.cpp: In member function ‘void MSA::ToPhyInterleavedFile(TextFile&) const’:
physeq.cpp:112: warning: comparison between signed and unsigned integer expressions
physeq.cpp:124: warning: comparison between signed and unsigned integer expressions
intmath.h: At global scope:
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c phytofile.cpp -o phytofile.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c posgap.cpp -o posgap.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c ppscore.cpp -o ppscore.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c profdb.cpp -o profdb.o
In file included from clustsetmsa.h:8,
                 from profdb.cpp:9:
msadist.h: In member function ‘double MSADist::ComputeDist(const MSA&, unsigned int, unsigned int)’:
msadist.h:22: warning: enumeration value ‘DISTANCE_Undefined’ not handled in switch
msadist.h:22: warning: enumeration value ‘DISTANCE_Kmer6_6’ not handled in switch
msadist.h:22: warning: enumeration value ‘DISTANCE_Kmer20_3’ not handled in switch
msadist.h:22: warning: enumeration value ‘DISTANCE_Kmer20_4’ not handled in switch
msadist.h:22: warning: enumeration value ‘DISTANCE_Kbit20_3’ not handled in switch
msadist.h:22: warning: enumeration value ‘DISTANCE_Kmer4_6’ not handled in switch
msadist.h:22: warning: enumeration value ‘DISTANCE_PWKimura’ not handled in switch
msadist.h:22: warning: enumeration value ‘DISTANCE_PWScoreDist’ not handled in switch
msadist.h:22: warning: enumeration value ‘DISTANCE_ScoreDist’ not handled in switch
msadist.h:22: warning: enumeration value ‘DISTANCE_Edit’ not handled in switch
intmath.h: At global scope:
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c profile.cpp -o profile.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c profilefrommsa.cpp -o profilefrommsa.o
profilefrommsa.cpp: In function ‘void ListProfile(const ProfPos*, unsigned int, const MSA*)’:
profilefrommsa.cpp:131: warning: comparison between signed and unsigned integer expressions
profilefrommsa.cpp: In function ‘unsigned int ResidueGroupFromFCounts(const FCOUNT*)’:
profilefrommsa.cpp:230: warning: enumeration value ‘ALPHA_Undefined’ not handled in switch
profilefrommsa.cpp: In function ‘ProfPos* ProfileFromMSA(const MSA&)’:
profilefrommsa.cpp:245: warning: unused variable ‘uSeqCount’
profilefrommsa.cpp:253: warning: unused variable ‘uHydrophobicRunLength’
intmath.h: At global scope:
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
profilefrommsa.cpp:15: warning: ‘const char* LocalScoreToStr(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c progalign.cpp -o progalign.o
progalign.cpp: In function ‘ProgNode* ProgressiveAlignE(const SeqVect&, const Tree&, MSA&)’:
progalign.cpp:41: warning: unused variable ‘uIterCount’
intmath.h: At global scope:
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c progress.cpp -o progress.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c progressivealign.cpp -o progressivealign.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c pwpath.cpp -o pwpath.o
pwpath.cpp: In member function ‘void PWPath::Validate() const’:
pwpath.cpp:80: warning: unused variable ‘LastEdge’
pwpath.cpp: In member function ‘void PWPath::FromFile(TextFile&)’:
pwpath.cpp:213: warning: unused variable ‘uEdgeIndex’
intmath.h: At global scope:
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c readmx.cpp -o readmx.o
readmx.cpp: In function ‘float (* ReadMx(TextFile&))[32][32]’:
readmx.cpp:83: warning: comparison between signed and unsigned integer expressions
readmx.cpp:84: warning: comparison between signed and unsigned integer expressions
readmx.cpp: In function ‘float (* ReadMxFromR(std::vector<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::basic_string<char, std::char_traits<char>, std::allocator<char> > > >, float (*)[32]))[32][32]’:
readmx.cpp:184: warning: comparison between signed and unsigned integer expressions
readmx.cpp:185: warning: comparison between signed and unsigned integer expressions
intmath.h: At global scope:
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
readmx.cpp:30: warning: ‘unsigned int MxCharToLetter(char)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c realigndiffs.cpp -o realigndiffs.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c realigndiffse.cpp -o realigndiffse.o
realigndiffse.cpp: In function ‘void RealignDiffsE(const MSA&, const SeqVect&, const Tree&, const Tree&, const unsigned int*, MSA&, ProgNode*)’:
realigndiffse.cpp:77: warning: unused variable ‘uNewRight’
realigndiffse.cpp:80: warning: unused variable ‘uOldRight’
intmath.h: At global scope:
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c refine.cpp -o refine.o
In file included from clustsetmsa.h:8,
                 from refine.cpp:9:
msadist.h: In member function ‘double MSADist::ComputeDist(const MSA&, unsigned int, unsigned int)’:
msadist.h:22: warning: enumeration value ‘DISTANCE_Undefined’ not handled in switch
msadist.h:22: warning: enumeration value ‘DISTANCE_Kmer6_6’ not handled in switch
msadist.h:22: warning: enumeration value ‘DISTANCE_Kmer20_3’ not handled in switch
msadist.h:22: warning: enumeration value ‘DISTANCE_Kmer20_4’ not handled in switch
msadist.h:22: warning: enumeration value ‘DISTANCE_Kbit20_3’ not handled in switch
msadist.h:22: warning: enumeration value ‘DISTANCE_Kmer4_6’ not handled in switch
msadist.h:22: warning: enumeration value ‘DISTANCE_PWKimura’ not handled in switch
msadist.h:22: warning: enumeration value ‘DISTANCE_PWScoreDist’ not handled in switch
msadist.h:22: warning: enumeration value ‘DISTANCE_ScoreDist’ not handled in switch
msadist.h:22: warning: enumeration value ‘DISTANCE_Edit’ not handled in switch
intmath.h: At global scope:
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c refinehoriz.cpp -o refinehoriz.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c refinesubfams.cpp -o refinesubfams.o
refinesubfams.cpp: In function ‘bool RefineSubfams(MSA&, const Tree&, unsigned int)’:
refinesubfams.cpp:63: warning: unused variable ‘uNodeCount’
intmath.h: At global scope:
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c refinetree.cpp -o refinetree.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c refinetreee.cpp -o refinetreee.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c refinevert.cpp -o refinevert.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c refinew.cpp -o refinew.o
refinew.cpp: In function ‘void AppendMSA(MSA&, const MSA&)’:
refinew.cpp:22: warning: unused variable ‘uColCountCat’
refinew.cpp: In function ‘void RefineW(const MSA&, MSA&)’:
refinew.cpp:125: warning: unused variable ‘uOutCols’
intmath.h: At global scope:
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c savebest.cpp -o savebest.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c scoredist.cpp -o scoredist.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c scoregaps.cpp -o scoregaps.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
scoregaps.cpp:37: warning: ‘void FreeGapInfo(GAPINFO*)’ defined but not used
scoregaps.cpp:80: warning: ‘SCORE Penalty(unsigned int, bool)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c scorehistory.cpp -o scorehistory.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c scorepp.cpp -o scorepp.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c seq.cpp -o seq.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c seqvect.cpp -o seqvect.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c setblosumweights.cpp -o setblosumweights.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c setgscweights.cpp -o setgscweights.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c setnewhandler.cpp -o setnewhandler.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c spfast.cpp -o spfast.o
spfast.cpp: In function ‘SCORE ObjScoreSPDimer(const MSA&)’:
spfast.cpp:252: warning: unused variable ‘uSeqCount’
intmath.h: At global scope:
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
spfast.cpp:14: warning: ‘const char* GapTypeToStr(int)’ defined but not used
spfast.cpp:59: warning: ‘SCORE SPColBrute(const MSA&, unsigned int)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c sptest.cpp -o sptest.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c stabilize.cpp -o stabilize.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c subfam.cpp -o subfam.o
subfam.cpp: In function ‘void AlignSubFam(SeqVect&, const Tree&, unsigned int, MSA&)’:
subfam.cpp:173: warning: unused variable ‘NotUsed’
intmath.h: At global scope:
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c subfams.cpp -o subfams.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
subfams.cpp:10: warning: ‘void GetMostDistantPair(DistFunc&, unsigned int*, unsigned int*)’ defined but not used
subfams.cpp:40: warning: ‘void InitializeSingleSource(DistFunc&, unsigned int)’ defined but not used
subfams.cpp:52: warning: ‘void Relax(DistFunc&, unsigned int, unsigned int)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c sw.cpp -o sw.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
sw.cpp:21: warning: ‘void ListDP(const SCORE*, const ProfPos*, const ProfPos*, unsigned int, unsigned int)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c termgaps.cpp -o termgaps.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c textfile.cpp -o textfile.o
textfile.cpp: In member function ‘void TextFile::PutChar(char)’:
textfile.cpp:111: warning: unused variable ‘i’
textfile.cpp: In member function ‘void TextFile::PutString(const char*)’:
textfile.cpp:124: warning: unused variable ‘iError’
intmath.h: At global scope:
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c threewaywt.cpp -o threewaywt.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c tomhydro.cpp -o tomhydro.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c traceback.cpp -o traceback.o
traceback.cpp: In function ‘SCORE TraceBack(const ProfPos*, unsigned int, const ProfPos*, unsigned int, const SCORE*, const SCORE*, const SCORE*, PWPath&)’:
traceback.cpp:21: warning: unused variable ‘uPrefixCountB’
intmath.h: At global scope:
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c tracebackopt.cpp -o tracebackopt.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c tracebacksw.cpp -o tracebacksw.o
tracebacksw.cpp: In function ‘void TraceBackSW(const ProfPos*, unsigned int, const ProfPos*, unsigned int, const SCORE*, const SCORE*, const SCORE*, unsigned int, unsigned int, PWPath&)’:
tracebacksw.cpp:22: warning: unused variable ‘uPrefixCountB’
tracebacksw.cpp:29: warning: unused variable ‘scoreMax’
intmath.h: At global scope:
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c treefrommsa.cpp -o treefrommsa.o
In file included from clustsetmsa.h:8,
                 from treefrommsa.cpp:5:
msadist.h: In member function ‘double MSADist::ComputeDist(const MSA&, unsigned int, unsigned int)’:
msadist.h:22: warning: enumeration value ‘DISTANCE_Undefined’ not handled in switch
msadist.h:22: warning: enumeration value ‘DISTANCE_Kmer6_6’ not handled in switch
msadist.h:22: warning: enumeration value ‘DISTANCE_Kmer20_3’ not handled in switch
msadist.h:22: warning: enumeration value ‘DISTANCE_Kmer20_4’ not handled in switch
msadist.h:22: warning: enumeration value ‘DISTANCE_Kbit20_3’ not handled in switch
msadist.h:22: warning: enumeration value ‘DISTANCE_Kmer4_6’ not handled in switch
msadist.h:22: warning: enumeration value ‘DISTANCE_PWKimura’ not handled in switch
msadist.h:22: warning: enumeration value ‘DISTANCE_PWScoreDist’ not handled in switch
msadist.h:22: warning: enumeration value ‘DISTANCE_ScoreDist’ not handled in switch
msadist.h:22: warning: enumeration value ‘DISTANCE_Edit’ not handled in switch
intmath.h: At global scope:
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c typetostr.cpp -o typetostr.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c upgma2.cpp -o upgma2.o
upgma2.cpp: In member function ‘virtual void DistCalcTest::CalcDistRange(unsigned int, dist_t*) const’:
upgma2.cpp:371: warning: missing braces around initializer for ‘dist_t [5]’
upgma2.cpp:371: warning: missing braces around initializer for ‘dist_t [5]’
upgma2.cpp:371: warning: missing braces around initializer for ‘dist_t [5]’
upgma2.cpp:371: warning: missing braces around initializer for ‘dist_t [5]’
upgma2.cpp:371: warning: missing braces around initializer for ‘dist_t [5]’
intmath.h: At global scope:
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
upgma2.cpp:68: warning: ‘void ListState()’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c usage.cpp -o usage.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c validateids.cpp -o validateids.o
In file included from validateids.cpp:4:
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c vtml2.cpp -o vtml2.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c writescorefile.cpp -o writescorefile.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c RMuscle.cpp -o RMuscle.o
intmath.h:59: warning: ‘double ScoreToDouble(SCORE)’ defined but not used
llvm-g++-4.2 -arch x86_64 -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 -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
/usr/bin/nm: no name list
/usr/bin/nm: no name list
/usr/bin/nm: no name list
/usr/bin/nm: no name list
/usr/bin/nm: no name list
/usr/bin/nm: no name list
/usr/bin/nm: no name list
/usr/bin/nm: no name list
/usr/bin/nm: no name list
/usr/bin/nm: no name list
/usr/bin/nm: no name list
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
/usr/bin/ranlib: file: libMuscle.a(blosumla.o) has no symbols
/usr/bin/ranlib: file: libMuscle.a(glbalign352.o) has no symbols
/usr/bin/ranlib: file: libMuscle.a(globalslinux.o) has no symbols
/usr/bin/ranlib: file: libMuscle.a(globalsother.o) has no symbols
/usr/bin/ranlib: file: libMuscle.a(globalswin32.o) has no symbols
/usr/bin/ranlib: file: libMuscle.a(nwdasimple2.o) has no symbols
/usr/bin/ranlib: file: libMuscle.a(nwdasmall.o) has no symbols
/usr/bin/ranlib: file: libMuscle.a(nwrec.o) has no symbols
/usr/bin/ranlib: file: libMuscle.a(objscoreda.o) has no symbols
/usr/bin/ranlib: file: libMuscle.a(pam200mafft.o) has no symbols
/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.  `Rscript -e "Rcpp:::CxxFlags()"`"; \
	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-darwin10.8.0
checking host system type... i386-apple-darwin10.8.0
checking target system type... i386-apple-darwin10.8.0
building for darwin10.8.0
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
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c pairwise/FullPairwiseAlign.cpp -o pairwise/FullPairwiseAlign.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c pairwise/FastPairwiseAlign.cpp -o pairwise/FastPairwiseAlign.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c fileInput/MSFFileParser.cpp -o fileInput/MSFFileParser.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c fileInput/FileReader.cpp -o fileInput/FileReader.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c fileInput/PIRFileParser.cpp -o fileInput/PIRFileParser.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c fileInput/RSFFileParser.cpp -o fileInput/RSFFileParser.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c fileInput/GDEFileParser.cpp -o fileInput/GDEFileParser.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c fileInput/InFileStream.cpp -o fileInput/InFileStream.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c fileInput/ClustalFileParser.cpp -o fileInput/ClustalFileParser.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c fileInput/PearsonFileParser.cpp -o fileInput/PearsonFileParser.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c fileInput/FileParser.cpp -o fileInput/FileParser.o
fileInput/FileParser.cpp: In member function ‘std::vector<clustalw::Sequence, std::allocator<clustalw::Sequence> > clustalw::FileParser::getSeqRangeR(int, int, std::string*, ClustalWInput*)’:
fileInput/FileParser.cpp:38: warning: unused variable ‘n’
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c fileInput/EMBLFileParser.cpp -o fileInput/EMBLFileParser.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c tree/UPGMA/RootedClusterTree.cpp -o tree/UPGMA/RootedClusterTree.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c tree/UPGMA/UPGMAAlgorithm.cpp -o tree/UPGMA/UPGMAAlgorithm.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c tree/UPGMA/Node.cpp -o tree/UPGMA/Node.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c tree/UPGMA/RootedGuideTree.cpp -o tree/UPGMA/RootedGuideTree.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c tree/UPGMA/RootedTreeOutput.cpp -o tree/UPGMA/RootedTreeOutput.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c tree/Tree.cpp -o tree/Tree.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c tree/ClusterTree.cpp -o tree/ClusterTree.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c tree/TreeInterface.cpp -o tree/TreeInterface.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c tree/UnRootedClusterTree.cpp -o tree/UnRootedClusterTree.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c tree/ClusterTreeOutput.cpp -o tree/ClusterTreeOutput.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c tree/RandomGenerator.cpp -o tree/RandomGenerator.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c tree/NJTree.cpp -o tree/NJTree.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c tree/AlignmentSteps.cpp -o tree/AlignmentSteps.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c interface/CommandLineParser.cpp -o interface/CommandLineParser.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c substitutionMatrix/SubMatrix.cpp -o substitutionMatrix/SubMatrix.o
substitutionMatrix/SubMatrix.cpp: In member function ‘int clustalw::SubMatrix::readMatrixSeriesFromR(Rcpp::NumericMatrix, clustalw::Matrix&, clustalw::Xref&)’:
substitutionMatrix/SubMatrix.cpp:1305: warning: unused variable ‘inline1’
substitutionMatrix/SubMatrix.cpp:1307: warning: unused variable ‘nmat’
substitutionMatrix/SubMatrix.cpp:1308: warning: unused variable ‘n’
substitutionMatrix/SubMatrix.cpp:1308: warning: unused variable ‘llimit’
substitutionMatrix/SubMatrix.cpp:1308: warning: unused variable ‘ulimit’
substitutionMatrix/SubMatrix.cpp: In member function ‘int clustalw::SubMatrix::readUserMatrixFromR(Rcpp::NumericMatrix, clustalw::Matrix&, clustalw::Xref&)’:
substitutionMatrix/SubMatrix.cpp:1361: warning: comparison between signed and unsigned integer expressions
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c multipleAlign/Iteration.cpp -o multipleAlign/Iteration.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c multipleAlign/MSA.cpp -o multipleAlign/MSA.o
multipleAlign/MSA.cpp: In member function ‘int clustalw::MSA::multiSeqAlign(clustalw::Alignment*, clustalw::DistMatrix*, std::vector<int, std::allocator<int> >*, clustalw::AlignmentSteps*, int)’:
multipleAlign/MSA.cpp:340: warning: unused variable ‘alignmentScore’
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c multipleAlign/MyersMillerProfileAlign.cpp -o multipleAlign/MyersMillerProfileAlign.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c multipleAlign/ProfileStandard.cpp -o multipleAlign/ProfileStandard.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c multipleAlign/ProfileWithSub.cpp -o multipleAlign/ProfileWithSub.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c multipleAlign/ProfileBase.cpp -o multipleAlign/ProfileBase.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c multipleAlign/LowScoreSegProfile.cpp -o multipleAlign/LowScoreSegProfile.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c general/OutputFile.cpp -o general/OutputFile.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c general/UserParameters.cpp -o general/UserParameters.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c general/Utility.cpp -o general/Utility.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c general/InvalidCombination.cpp -o general/InvalidCombination.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c general/DebugLog.cpp -o general/DebugLog.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c general/ClustalWResources.cpp -o general/ClustalWResources.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c general/VectorOutOfRange.cpp -o general/VectorOutOfRange.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c general/SymMatrix.cpp -o general/SymMatrix.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c general/Stats.cpp -o general/Stats.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c Help.cpp -o Help.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c alignment/Alignment.cpp -o alignment/Alignment.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c alignment/AlignmentOutput.cpp -o alignment/AlignmentOutput.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c alignment/ObjectiveScore.cpp -o alignment/ObjectiveScore.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c alignment/Sequence.cpp -o alignment/Sequence.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c Clustal.cpp -o Clustal.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c RClustalWMain.cpp -o RClustalWMain.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"  -DHAVE_CONFIG_H -I.  -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c RClustalW.cpp -o RClustalW.o
llvm-g++-4.2 -arch x86_64 -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 -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
----------------------------------------
--------------- ClustalW ---------------
----------------------------------------
--------- Compilation finished ---------
----------------------------------------
make --file=msaMakefile --directory=ClustalOmega
./configure `Rscript -e "if (Sys.info()['sysname'] == 'Darwin') cat('--without-openmp')"`; \
	export PKG_LIBS=" "; \
	export PKG_CXXFLAGS="  -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I"../../gc-7.2/include" `Rscript -e "Rcpp:::CxxFlags()"`"; \
	export PKG_CFLAGS="  -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I"../../gc-7.2/include" `Rscript -e "Rcpp:::CxxFlags()"`"; \
	cd src; \
	R CMD SHLIB -o libClustalOmega.so exceptions4c/e4c_lite.c argtable2/argtable2.c argtable2/arg_end.c argtable2/arg_rem.c argtable2/arg_lit.c argtable2/arg_int.c argtable2/arg_dbl.c argtable2/arg_str.c argtable2/arg_file.c kmpp/KMeans.cpp kmpp/KmTree.cpp kmpp/KmUtils.cpp clustal/hhalign_wrapper.c clustal/ktuple_pair.c clustal/list.c clustal/log.c clustal/muscle_upgma.c clustal/muscle_tree.c clustal/mbed.c clustal/pair_dist.c clustal/progress.c clustal/seq.c clustal/symmatrix.c clustal/tree.c clustal/util.c clustal/weights.c squid/a2m.c squid/aligneval.c squid/alignio.c squid/clustal.c squid/cluster.c squid/dayhoff.c squid/eps.c squid/file.c squid/getopt.c squid/gki.c squid/gsi.c squid/gsi64.c squid/hsregex.c squid/iupac.c squid/msa.c squid/msf.c squid/phylip.c squid/revcomp.c squid/rk.c squid/selex.c squid/seqencode.c squid/shuffle.c squid/sqerror.c squid/sqio.c squid/squidcore.c squid/sre_ctype.c squid/sre_math.c squid/sre_random.c squid/sre_string.c squid/ssi.c squid/stack.c squid/stockholm.c squid/stopwatch.c squid/translate.c squid/types.c squid/vectorops.c squid/weight.c hhalign/hhalign.cpp RClustalOmega.cpp mymain.c clustal-omega.c && \
	ar rcs libClustalOmega.a exceptions4c/e4c_lite.o argtable2/argtable2.o argtable2/arg_end.o argtable2/arg_rem.o argtable2/arg_lit.o argtable2/arg_int.o argtable2/arg_dbl.o argtable2/arg_str.o argtable2/arg_file.o kmpp/KMeans.o kmpp/KmTree.o kmpp/KmUtils.o clustal/hhalign_wrapper.o clustal/ktuple_pair.o clustal/list.o clustal/log.o clustal/muscle_upgma.o clustal/muscle_tree.o clustal/mbed.o clustal/pair_dist.o clustal/progress.o clustal/seq.o clustal/symmatrix.o clustal/tree.o clustal/util.o clustal/weights.o squid/a2m.o squid/aligneval.o squid/alignio.o squid/clustal.o squid/cluster.o squid/dayhoff.o squid/eps.o squid/file.o squid/getopt.o squid/gki.o squid/gsi.o squid/gsi64.o squid/hsregex.o squid/iupac.o squid/msa.o squid/msf.o squid/phylip.o squid/revcomp.o squid/rk.o squid/selex.o squid/seqencode.o squid/shuffle.o squid/sqerror.o squid/sqio.o squid/squidcore.o squid/sre_ctype.o squid/sre_math.o squid/sre_random.o squid/sre_string.o squid/ssi.o squid/stack.o squid/stockholm.o squid/stopwatch.o squid/translate.o squid/types.o squid/vectorops.o squid/weight.o hhalign/hhalign.o RClustalOmega.o mymain.o clustal-omega.o && \
	cp libClustalOmega.a ../../
configure:

    Welcome to Clustal Omega - version 1.2.0 (AndreaGiacomo)

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

              
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
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checking for C compiler default output file name... a.out
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 for gcc option to accept ISO C89... none needed
checking dependency style of gcc... gcc3
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /usr/bin/grep
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checking minix/config.h usability... no
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checking build system type... i386-apple-darwin10.8.0
checking host system type... i386-apple-darwin10.8.0
checking whether make sets $(MAKE)... (cached) yes
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checking for ld used by gcc... /usr/llvm-gcc-4.2/libexec/gcc/i686-apple-darwin10/4.2.1/ld
checking if the linker (/usr/llvm-gcc-4.2/libexec/gcc/i686-apple-darwin10/4.2.1/ld) is GNU ld... no
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checking the name lister (/usr/bin/nm) interface... BSD nm
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checking for /usr/llvm-gcc-4.2/libexec/gcc/i686-apple-darwin10/4.2.1/ld option to reload object files... -r
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checking command to parse /usr/bin/nm 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 (/usr/llvm-gcc-4.2/libexec/gcc/i686-apple-darwin10/4.2.1/ld) supports shared libraries... yes
checking dynamic linker characteristics... darwin10.8.0 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
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checking dependency style of g++... (cached) gcc3
checking how to run the C++ preprocessor... g++ -E
checking for ld used by g++... /usr/llvm-gcc-4.2/libexec/gcc/i686-apple-darwin10/4.2.1/ld
checking if the linker (/usr/llvm-gcc-4.2/libexec/gcc/i686-apple-darwin10/4.2.1/ld) is GNU ld... no
checking whether the g++ linker (/usr/llvm-gcc-4.2/libexec/gcc/i686-apple-darwin10/4.2.1/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 (/usr/llvm-gcc-4.2/libexec/gcc/i686-apple-darwin10/4.2.1/ld) supports shared libraries... yes
checking dynamic linker characteristics... darwin10.8.0 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 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: src/clustal-omega-config.h is unchanged
config.status: executing depfiles commands
config.status: executing libtool commands
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c exceptions4c/e4c_lite.c -o exceptions4c/e4c_lite.o
exceptions4c/e4c_lite.c:16: warning: missing braces around initializer
exceptions4c/e4c_lite.c:16: warning: (near initialization for ‘e4c.jump’)
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c argtable2/argtable2.c -o argtable2/argtable2.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c argtable2/arg_end.c -o argtable2/arg_end.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c argtable2/arg_rem.c -o argtable2/arg_rem.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c argtable2/arg_lit.c -o argtable2/arg_lit.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c argtable2/arg_int.c -o argtable2/arg_int.o
argtable2/arg_int.c: In function ‘strtol0X’:
argtable2/arg_int.c:60: warning: implicit declaration of function ‘isspace’
argtable2/arg_int.c:89: warning: implicit declaration of function ‘toupper’
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c argtable2/arg_dbl.c -o argtable2/arg_dbl.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c argtable2/arg_str.c -o argtable2/arg_str.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c argtable2/arg_file.c -o argtable2/arg_file.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c kmpp/KMeans.cpp -o kmpp/KMeans.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c kmpp/KmTree.cpp -o kmpp/KmTree.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c kmpp/KmUtils.cpp -o kmpp/KmUtils.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c clustal/hhalign_wrapper.c -o clustal/hhalign_wrapper.o
In file included from clustal/hhalign_wrapper.c:22:
./config.h:132:1: warning: "NDEBUG" redefined
<command-line>: warning: this is the location of the previous definition
clustal/hhalign_wrapper.c: In function ‘SanitiseUnknown’:
clustal/hhalign_wrapper.c:85: warning: unused variable ‘iLen’
clustal/hhalign_wrapper.c:84: warning: unused variable ‘iR’
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c clustal/ktuple_pair.c -o clustal/ktuple_pair.o
In file included from clustal/ktuple_pair.c:29:
./config.h:132:1: warning: "NDEBUG" redefined
<command-line>: warning: this is the location of the previous definition
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c clustal/list.c -o clustal/list.o
In file included from clustal/list.c:32:
./config.h:132:1: warning: "NDEBUG" redefined
<command-line>: warning: this is the location of the previous definition
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c clustal/log.c -o clustal/log.o
In file included from clustal/log.c:22:
./config.h:132:1: warning: "NDEBUG" redefined
<command-line>: warning: this is the location of the previous definition
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c clustal/muscle_upgma.c -o clustal/muscle_upgma.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c clustal/muscle_tree.c -o clustal/muscle_tree.o
clustal/muscle_tree.c:520: warning: ‘IsEdge’ defined but not used
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c clustal/mbed.c -o clustal/mbed.o
In file included from clustal/mbed.c:28:
./config.h:132:1: warning: "NDEBUG" redefined
<command-line>: warning: this is the location of the previous definition
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c clustal/pair_dist.c -o clustal/pair_dist.o
In file included from clustal/pair_dist.c:22:
./config.h:132:1: warning: "NDEBUG" redefined
<command-line>: warning: this is the location of the previous definition
clustal/pair_dist.c: In function ‘SquidIdPairDist’:
clustal/pair_dist.c:177: warning: unused variable ‘bPrintCR’
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c clustal/progress.c -o clustal/progress.o
In file included from clustal/progress.c:22:
./config.h:132:1: warning: "NDEBUG" redefined
<command-line>: warning: this is the location of the previous definition
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c clustal/seq.c -o clustal/seq.o
In file included from clustal/seq.c:30:
./config.h:132:1: warning: "NDEBUG" redefined
<command-line>: warning: this is the location of the previous definition
clustal/seq.c: In function ‘AliStat’:
clustal/seq.c:68: warning: unused variable ‘iAux’
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c clustal/symmatrix.c -o clustal/symmatrix.o
In file included from clustal/symmatrix.c:30:
./config.h:132:1: warning: "NDEBUG" redefined
<command-line>: warning: this is the location of the previous definition
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c clustal/tree.c -o clustal/tree.o
In file included from clustal/tree.c:22:
./config.h:132:1: warning: "NDEBUG" redefined
<command-line>: warning: this is the location of the previous definition
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c clustal/util.c -o clustal/util.o
In file included from clustal/util.c:22:
./config.h:132:1: warning: "NDEBUG" redefined
<command-line>: warning: this is the location of the previous definition
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c clustal/weights.c -o clustal/weights.o
In file included from clustal/weights.c:72:
./config.h:132:1: warning: "NDEBUG" redefined
<command-line>: warning: this is the location of the previous definition
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c squid/a2m.c -o squid/a2m.o
In file included from squid/squid.h:32,
                 from squid/a2m.c:20:
squid/../config.h:132:1: warning: "NDEBUG" redefined
<command-line>: warning: this is the location of the previous definition
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c squid/aligneval.c -o squid/aligneval.o
In file included from squid/squid.h:32,
                 from squid/aligneval.c:59:
squid/../config.h:132:1: warning: "NDEBUG" redefined
<command-line>: warning: this is the location of the previous definition
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c squid/alignio.c -o squid/alignio.o
In file included from squid/squid.h:32,
                 from squid/alignio.c:21:
squid/../config.h:132:1: warning: "NDEBUG" redefined
<command-line>: warning: this is the location of the previous definition
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c squid/clustal.c -o squid/clustal.o
In file included from squid/squid.h:32,
                 from squid/clustal.c:24:
squid/../config.h:132:1: warning: "NDEBUG" redefined
<command-line>: warning: this is the location of the previous definition
squid/clustal.c: In function ‘WriteClustal’:
squid/clustal.c:214: warning: unused variable ‘cons’
squid/clustal.c: In function ‘WriteClustalForR’:
squid/clustal.c:438: warning: unused variable ‘cons’
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c squid/cluster.c -o squid/cluster.o
In file included from squid/squid.h:32,
                 from squid/cluster.c:124:
squid/../config.h:132:1: warning: "NDEBUG" redefined
<command-line>: warning: this is the location of the previous definition
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c squid/dayhoff.c -o squid/dayhoff.o
In file included from squid/squid.h:32,
                 from squid/dayhoff.c:28:
squid/../config.h:132:1: warning: "NDEBUG" redefined
<command-line>: warning: this is the location of the previous definition
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c squid/eps.c -o squid/eps.o
In file included from squid/squid.h:32,
                 from squid/eps.c:23:
squid/../config.h:132:1: warning: "NDEBUG" redefined
<command-line>: warning: this is the location of the previous definition
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c squid/file.c -o squid/file.o
In file included from squid/squid.h:32,
                 from squid/file.c:28:
squid/../config.h:132:1: warning: "NDEBUG" redefined
<command-line>: warning: this is the location of the previous definition
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c squid/getopt.c -o squid/getopt.o
In file included from squid/squid.h:32,
                 from squid/getopt.c:17:
squid/../config.h:132:1: warning: "NDEBUG" redefined
<command-line>: warning: this is the location of the previous definition
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c squid/gki.c -o squid/gki.o
In file included from squid/squid.h:32,
                 from squid/gki.c:82:
squid/../config.h:132:1: warning: "NDEBUG" redefined
<command-line>: warning: this is the location of the previous definition
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c squid/gsi.c -o squid/gsi.o
In file included from squid/squid.h:32,
                 from squid/gsi.c:35:
squid/../config.h:132:1: warning: "NDEBUG" redefined
<command-line>: warning: this is the location of the previous definition
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c squid/gsi64.c -o squid/gsi64.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c squid/hsregex.c -o squid/hsregex.o
In file included from squid/squid.h:32,
                 from squid/hsregex.c:33:
squid/../config.h:132:1: warning: "NDEBUG" redefined
<command-line>: warning: this is the location of the previous definition
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c squid/iupac.c -o squid/iupac.o
In file included from squid/squid.h:32,
                 from squid/iupac.c:17:
squid/../config.h:132:1: warning: "NDEBUG" redefined
<command-line>: warning: this is the location of the previous definition
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c squid/msa.c -o squid/msa.o
In file included from squid/squid.h:32,
                 from squid/msa.c:22:
squid/../config.h:132:1: warning: "NDEBUG" redefined
<command-line>: warning: this is the location of the previous definition
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c squid/msf.c -o squid/msf.o
In file included from squid/squid.h:32,
                 from squid/msf.c:25:
squid/../config.h:132:1: warning: "NDEBUG" redefined
<command-line>: warning: this is the location of the previous definition
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c squid/phylip.c -o squid/phylip.o
In file included from squid/squid.h:32,
                 from squid/phylip.c:23:
squid/../config.h:132:1: warning: "NDEBUG" redefined
<command-line>: warning: this is the location of the previous definition
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c squid/revcomp.c -o squid/revcomp.o
In file included from squid/squid.h:32,
                 from squid/revcomp.c:19:
squid/../config.h:132:1: warning: "NDEBUG" redefined
<command-line>: warning: this is the location of the previous definition
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c squid/rk.c -o squid/rk.o
In file included from squid/squid.h:32,
                 from squid/rk.c:26:
squid/../config.h:132:1: warning: "NDEBUG" redefined
<command-line>: warning: this is the location of the previous definition
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c squid/selex.c -o squid/selex.o
In file included from squid/squid.h:32,
                 from squid/selex.c:43:
squid/../config.h:132:1: warning: "NDEBUG" redefined
<command-line>: warning: this is the location of the previous definition
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c squid/seqencode.c -o squid/seqencode.o
In file included from squid/squid.h:32,
                 from squid/seqencode.c:18:
squid/../config.h:132:1: warning: "NDEBUG" redefined
<command-line>: warning: this is the location of the previous definition
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c squid/shuffle.c -o squid/shuffle.o
In file included from squid/squid.h:32,
                 from squid/shuffle.c:42:
squid/../config.h:132:1: warning: "NDEBUG" redefined
<command-line>: warning: this is the location of the previous definition
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c squid/sqerror.c -o squid/sqerror.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c squid/sqio.c -o squid/sqio.o
In file included from squid/squid.h:32,
                 from squid/sqio.c:57:
squid/../config.h:132:1: warning: "NDEBUG" redefined
<command-line>: warning: this is the location of the previous definition
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c squid/squidcore.c -o squid/squidcore.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c squid/sre_ctype.c -o squid/sre_ctype.o
In file included from squid/squid.h:32,
                 from squid/sre_ctype.c:19:
squid/../config.h:132:1: warning: "NDEBUG" redefined
<command-line>: warning: this is the location of the previous definition
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c squid/sre_math.c -o squid/sre_math.o
In file included from squid/squid.h:32,
                 from squid/sre_math.c:19:
squid/../config.h:132:1: warning: "NDEBUG" redefined
<command-line>: warning: this is the location of the previous definition
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c squid/sre_random.c -o squid/sre_random.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c squid/sre_string.c -o squid/sre_string.o
In file included from squid/squid.h:32,
                 from squid/sre_string.c:23:
squid/../config.h:132:1: warning: "NDEBUG" redefined
<command-line>: warning: this is the location of the previous definition
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c squid/ssi.c -o squid/ssi.o
In file included from squid/squid.h:32,
                 from squid/ssi.c:16:
squid/../config.h:132:1: warning: "NDEBUG" redefined
<command-line>: warning: this is the location of the previous definition
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c squid/stack.c -o squid/stack.o
In file included from squid/squid.h:32,
                 from squid/stack.c:18:
squid/../config.h:132:1: warning: "NDEBUG" redefined
<command-line>: warning: this is the location of the previous definition
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c squid/stockholm.c -o squid/stockholm.o
In file included from squid/squid.h:32,
                 from squid/stockholm.c:31:
squid/../config.h:132:1: warning: "NDEBUG" redefined
<command-line>: warning: this is the location of the previous definition
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c squid/stopwatch.c -o squid/stopwatch.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c squid/translate.c -o squid/translate.o
In file included from squid/squid.h:32,
                 from squid/translate.c:19:
squid/../config.h:132:1: warning: "NDEBUG" redefined
<command-line>: warning: this is the location of the previous definition
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c squid/types.c -o squid/types.o
In file included from squid/squid.h:32,
                 from squid/types.c:20:
squid/../config.h:132:1: warning: "NDEBUG" redefined
<command-line>: warning: this is the location of the previous definition
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c squid/vectorops.c -o squid/vectorops.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c squid/weight.c -o squid/weight.o
In file included from squid/squid.h:32,
                 from squid/weight.c:19:
squid/../config.h:132:1: warning: "NDEBUG" redefined
<command-line>: warning: this is the location of the previous definition
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c hhalign/hhalign.cpp -o hhalign/hhalign.o
In file included from hhalign/hhalign.cpp:76:
hhalign/hhfunc-C.h: In function ‘void AddBackgroundFrequencies(float**, float**, float**, int, hmm_light*, char**, char*, int, char*)’:
hhalign/hhfunc-C.h:74: warning: unused variable ‘iT’
hhalign/hhfunc-C.h:80: warning: unused variable ‘fGThgiew’
hhalign/hhfunc-C.h:85: warning: unused variable ‘zf1SeqTrans’
hhalign/hhfunc-C.h:86: warning: unused variable ‘zf1SeqInit’
hhalign/hhfunc-C.h:87: warning: unused variable ‘zf1SeqDel’
hhalign/hhfunc-C.h:88: warning: unused variable ‘zf1SeqRevrt’
hhalign/hhfunc-C.h: In function ‘int ReadAndPrepare(int, char**, int, hmm_light*, char*, char*, double*, char*, HMM&, Alignment*)’:
hhalign/hhfunc-C.h:328: warning: unused variable ‘NEFF_SCORE’
hhalign/hhfunc-C.h:511: warning: unused variable ‘NEFF_SCORE’
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c RClustalOmega.cpp -o RClustalOmega.o
In file included from RClustalOmega.cpp:27:
config.h:132:1: warning: "NDEBUG" redefined
<command-line>: warning: this is the location of the previous definition
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c mymain.c -o mymain.o
In file included from mymain.c:22:
config.h:132:1: warning: "NDEBUG" redefined
<command-line>: warning: this is the location of the previous definition
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"    -fPIC -DHAVE_CONFIG_H -I. -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -I../../gc-7.2/include -I/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include -fPIC  -mtune=core2 -g -O2 -Wall  -c clustal-omega.c -o clustal-omega.o
In file included from clustal-omega.c:22:
config.h:132:1: warning: "NDEBUG" redefined
<command-line>: warning: this is the location of the previous definition
llvm-g++-4.2 -arch x86_64 -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 -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
/usr/bin/nm: no name list
/usr/bin/ranlib: file: libClustalOmega.a(gsi64.o) has no symbols
----------------------------------------
------------- ClustalOmega -------------
----------------------------------------
--------- Compilation finished ---------
----------------------------------------
llvm-g++-4.2 -arch x86_64 -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 -L/usr/local/lib -o msa.so R_init_msa.o -Wl,-all_load ./libgc.a ./libClustalW.a ./libClustalOmega.a ./libMuscle.a -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.1-bioc/meat/msa.Rcheck/msa/libs
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘print’ from package ‘base’ in package ‘msa’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (msa)

name	user	system	elapsed
MsaMetaData-class	0.647	0.015	0.663
MsaMultipleAlignmentClasses	0.499	0.007	0.506
msa-package	0.509	0.002	0.512
msa	1.172	0.008	1.181
msaClustalOmega	0.788	0.008	0.797
msaClustalW	1.040	0.005	1.046
msaMuscle	0.605	0.005	0.611
msaPrettyPrint	8.366	0.184	8.870